Someone in the past had the same issue. Here was my responce...
Sounds like it could be a few things. It could be an allergy such as an enviromental or food allergy causing your dog's ears to itch. Could also be fleas. Has your vet looked at this? If not I'd recommend going to the vet and having him or her take a look/take necessary tests. Meanwhile, here's some info I found online that could be the cause. You may want to suggests these to your vet as well;
In addition to allergies, there are other diseases which can cause your dog to scratch, lick, or pull on his hair. A short description of these conditions such as mange, cancer, behavioral problems, and infections, along with their diagnosis and treatment, are included in the table below. Many of the more uncommon conditions are listed as well. This large number of conditions helps you understand why a quick diagnosis may be difficult to make and various diagnostic tests may need to be performed. The most common conditions causing licking and scratching are color-coded gray in the table (some may be more common in certain geographical areas).
Condition Description
Symptoms
Diagnosis
Treatment
Acanthosis nigricans Inherited form seen in Dachshunds; secondary form caused by friction, hormonal abnormalities, or hypersensitivities Darkening of the skin; in secondary form see scratching and hair loss History, physical exam; in secondary form, testing to determine underlying cause Primary: No treatment; Secondary: Treat underlying disease; in some cases, steroids and Vitamin E supplementation
Acral lick dermatitis (neurodermatitis)
Self-licking in dogs results in self-trauma; possible causes include anxiety, boredom, stress (e.g., new member in household); licking can develop into an
obsessive behavior
Red, hairless, well-circumscribed, sometimes raised lesion usually on the leg; if chronic, will drain
Exclude other causes; history important
Relieve underlying cause e.g., anxiety; restrict licking, e.g., Elizabethan collar; behavior modifying medication may be necessary
Allergic and irritant contact dermatitis
An allergic reaction following exposure to antibiotics applied to the skin; metals such as nickel; materials such as rubber, wool, and plastic; and chemicals such as dyes and carpet deodorizers; or inflammation caused by irritating substances such as poison ivy. Generally requires multiple exposures.
Red skin and small bumps or blisters on the areas of skin that are sparsely haired and directly exposed to the offending substance; itching; hair loss in chronic conditions
Patch test, exclusion trials
Restrict exposure to the allergen or contact irritant in the dog's environment; steroids, antihistamines
Atopy (allergic inhalant dermatitis)
Allergic reaction to something airborne, such as pollen, house dust mites, and mold
Licking of feet, inflamed ears, itching, redness, and hair loss; sometimes development of infection or hot spots
Intradermal or serologic (blood) testing for allergies
Reduce exposure to allergen (what the dog is allergic to); steroids, fatty acid supplements, biotin, antihistamines, shampoos, or immunotherapy
Bacterial infection (pyoderma)
See Folliculitis, Staph hypersensitivity
Often occurs as a result of another condition such as a parasite, allergic, or hormonal condition
Bee, wasp, hornet stings Skin reactions can vary dramatically in severity Immediately after the bite, see swelling, redness, pain, possibly itching; subsequently may develop extensive ulcers with draining; may develop hives or anaphylaxis History, physical exam Antihistamines, steroids; wet dressings, if ulcerated; protect the area from self-inflicted trauma
Calcinosis cutis Mineralization of the skin usually due to an excess of corticosteroids; also rarely occurs in kidney failure, or in granulomas and tumors Hard nodules and papules usually on the back, groin, or axilla ulcerate, drain, and develop crusts; severe itching; may become infected; often see other signs of Cushing's disease Skin scrapings, biopsy, history, and other clinical signs, adrenal gland function tests If due to glandular tumors, selegiline, o,p-DDD (Mitotane), or surgical removal of tumor; if due to high steroid doses, withdraw use of steroids slowly
Cheyletiella (rabbit fur mite) mange
Infection with the Cheyletiella mite
Itching, scaliness; some hair loss, if severe
Skin scraping and microscopic examination - the mite is often very difficult to find Pyrethrin, Permethrin (Do NOT use permethrin on cats.)
Chiggers (harvest mites)
Seasonal disease caused by larvae of the chigger
Itching, bumps usually on feet, abdomen, folds at base of ears
Visualization of mite larvae or microscopic examination of skin scraping
Pyrethrin, Permethrin (Do NOT use permethrin on cats.)
Demodectic mange(red mange, puppy mange)
Infection with the Demodex mite - occurs when the immune system is deficient
Hair loss, scaliness, redness, pustules, ulcers, sometimes itching, darkening of the skin
Skin scraping and microscopic examination
NO Steroids
Amitraz (Mitaban) dips
Drug or injection reaction Rare skin reaction to a drug which is inhaled, given orally, or applied topically; more common with penicillins, sulfonamides, and cephalosporins; usually occurs within 2 weeks of giving the drug Can vary widely and may include itching, hair loss, redness, swelling, papules, crusts, ulcers, and draining wounds History of being treated with a drug, symptoms, biopsy Discontinue offending drug; treat symptomatically
Ear mites
Infection with Otodectes
Intense itching of ears, redness, dark crumbly discharge in ears
Direct visual or microscopic examination of ear discharge
Clean ears and apply medication containing pyrethrin (Ear Miticide)
Epitheliotropic lymphoma (mycosis fungoides) Rare cancer of T lymphocytes seen in older dogs Can take multiple forms: redness with itching and scale; ulcers and loss of pigment; one or more nodules; oral ulcers Needle or other biopsy Poor response to treatments, which include chemotherapy, surgical removal, retinoids, fatty acids
Flea allergy dermatitis (flea bite hypersensitivity)
Severe reaction by the animal to the saliva of the flea
Intense itching, redness, hair loss, papules, crusts, and scales; sometimes development of infection or hot spots
Presence of fleas; reaction to intradermal testing
Flea control in the environment and on the dog; steroids and antihistamines for the itching
Folliculitis Infection of the hair follicles, often with staph bacteria; symptoms usually appear on skin with less hair, such as the abdomen (belly) Pustules form in follicles and break open to form 'bull's-eye,' 'annular,' and 'target lesions,' which have crusty centers and red or darkening on the periphery, and 'epidermal collarettes,' which appear as rings of scaly skin; itching may occur; short-coated breeds may develop small tufts of hair which are lost; breeds with long coats may have seborrhea Skin scraping; culture; biopsy Antibiotics for at least 4 weeks - continue antibiotics 10 days beyond the apparent cure; if recurs, look for underlying problem such as allergy or hormonal imbalance
Food Allergies
Allergic reaction to something in the diet
Licking of feet, inflamed ears, itching, redness, and hair loss; sometimes development of infection or hot spots
Food elimination trials
Change in diet
Hookworms
Infection with the larvae (immature forms) of hookworms
Red bumps, usually on feet, rough foot pads, abnormal nail growth, itching
Physical exam, history of poor sanitation
Treat for intestinal infection; move dog to different environment
Hot spots (acute moist dermatitis)
Result from allergies, flea bites, mange, anal gland disease, poor grooming, ear infections, plant awns or burrs, arthritis
Hair loss; red, moist, oozing skin; constant licking or scratching
Physical exam and history
Treat underlying condition; clean area; apply Domeboro solution; topical and/or oral antibiotics and steroids
Lice
Infection with several species of lice
Variable; itching, hair loss, crusts, rough hair coat
Finding lice or nits on skin or hair
Pyrethrin, ivermectin (off-label use*), Permethrin (Do NOT use permethrin on cats.)
Lymphoma
Common cancer in dogs; can involve the skin
Itching, ulcers, nodules, redness
Biopsy
Surgery, chemotherapy, radiation; lymphoma of the skin does not usually respond to treatment as well as other lymphomas
Malassezia
Usually follows some other underlying disease
Itching, redness, hair loss, greasy scales; if chronic, develop
hyperpigmentation
Skin scraping/smear and microscopic examination, culture
Treat underlying disease; oral ketoconazole; miconazole shampoos
Here is another thread where someone had this issue and I gave some advice and other people gave some great advice too...
Itchy dog