The invention provides a method for preparing a special compound biological medicine fertilizer for apple trees, which comprises the following raw materials in parts by weight: 30-40 parts of kitchen wastes, 20-30 parts of tobacco straws, 10-15 parts of plant ash, 10-15 parts of distillers' grains, 16-18 parts of potassium humate, 10-12 parts of bird feathers, 18-22 parts of modified fly ash, 12-14 parts of urea, 11-13 parts of ammonia water, 14-16 parts of diammonium phosphate, 13-15 parts of potassium sulfate, 11-13 parts of calcium superphosphate, 2-4 parts of cnidium fruit, 2-4 parts of aloe, 3-5 parts of eucalyptus leaves, 2-4 parts of pharbitis seed, 3-5 parts of cyrtomium rhizome, 0.5-0.8 part of zinc sulfate, 0.8-1.0 part of magnesium sulfate, 0.7-0.9 part of boric acid, 0.4-0.6 part of fermentation preparation and a proper amount of citronella oil. After various organic wastes are mixed and fermented to produce green organic fertilizers, the environmental pollution is reduced, the fermented organic matter is mixed with the inorganic fertilizer, the Chinese herbal medicine juice (citronella oil) with insecticide properties is added, the nutrition is more comprehensive, and the bactericidal effect is increased; the fertilizer has the advantages of obviously improved fertilizer utilization ratio, single time of application, effective slow release, reduced fertilization frequency, reduced fertilizer cost and improved economic benefit; and after the application of the fertilizer, the quality of the apple trees can be effectively improved, and the yield can be improved.