The invention discloses carbon-based fertilizer specially used for an apple tree and application thereof. Raw materials of the fertilizer contain corncob pellet carbon microparticles, urea, monoammonium phosphate, potassium sulfate, borax, zinc sulfate, copper sulfate, manganese sulfate and ferrous sulfate. According to the invention, abundant micropores and stronger adsorption property of the corncob pellet carbon are utilized, the corncob pellet carbon is compounded with nitrogen, phosphorous and potassium as well as other nutrient elements which are required for growth and development of apple, and bentonite or clay is taken as a binder, so that the granular carbon-based fertilizer specially used for the apple tree is obtained. The fertilizer disclosed by the invention is simple in preparation technology, economic and environment-friendly, nutrient requirements of different tree ages and different apple growth periods are met, and fertilizer utilization rate is high, so that fertilization cost and energy consumption are saved, fruit yield and quality of apples are beneficially improved, and the carbon-based fertilizer specially used for the apple tree is applicable to being popularized and applied in wide areas.