The invention discloses a chemical fertilizer special for coix seed and a preparation method thereof. The chemical fertilizer is prepared from the following ingredients in parts by mass: 26-28 parts of nitrogen fertilizer, 22-24 parts of phosphate fertilizer, 18-20 parts of potassium fertilizer, 15-17 parts of castor seed cake, 12-14 parts of rhizobium fertilizer, 9-11 parts of yeast fertilizer, 6-8 parts of vicia villosa green fertilizer, 2-4 parts of biogas waste fertilizer, 5-7 parts of monoammonium phosphate, 6-9 parts of magnesium sulfate, 3-5 parts of copper ammonium phosphate, 1-3 parts of calcium chloride, 4-6 parts of manganese chloride, 8-10 parts of organic complexing iron and 50-70 parts of water. The chemical fertilizer is rich in nutritional substances, can be prepared simply, has low cost, and can effectively promote strong growth of coix seed, and the coix seeds are full, white, smooth and tough in texture; and besides, the chemical fertilizer can improve the soil due to the vicia villosa green fertilizer in the formula, and can greatly improve the yield and the quality of the coix seed.