The invention provides a disease prevention selenium-rich compound fertilizer capable of improving apple tree planting soil and a preparation method of the disease prevention selenium-rich compound fertilizer.The compound fertilizer comprises, by weight, urea, organic fertilizer, ammonium dihydrogen phosphate, monoammonium phosphate, potassium chloride, zinc sulfate, humic acid, attapulgite, sodium selenite, an EM microbial agent, EDTA chelate iron, EDTA chelate zinc, EDTA chelate copper, humic acid urea iron, humic acid magnesium, a urease inhibitor, a nitrification inhibitor and multi-effect triazole.The compound fertilizer is an organic-inorganic compound fertilizer, the effective period is long, the fertilizer is rich in microelement, the varieties and content of nutrient elements in the soil can be increased, and the nutritional value of apples is improved; a microbial strain and fungicide are contained and combined, so that the disease prevention capacity in the apple tree planting process is improved, the fertilizer components are friendly to the soil, soil quality can be improved, the content of organic matter in the soil is increased, the quality of the apples is improved, the yield of the apples is increased, the production cost is low, market promotion is promoted, and economic benefits are good.