The invention discloses an active phosphate fertilizer as well as a preparation method and application thereof, and belongs to the fertilizer industrial field. The active phosphate fertilizer adopts waste animal protein (furs, hairs, skins or horns and the like) as a raw material; the animal protein is hydrolyzed by using mixed acid to obtain amino acid residues, wherein the mixed acid comprises hydrochloric acid, nitric acid and sulfuric acid; the residues are mixed with ground phosphate rock; alkali substances, such as lime, magnesium oxide and the like are added; and materials, such as decomposed coal, kieselguhr and the like are added for modifying; then the materials are turned, composted for several days, dried and smashed to obtain the active phosphate fertilizer. The active phosphate fertilizer has rich contents of organic matters, N, P, Ca and Mg, high contents of water-soluble phosphorus and available phosphorus and reasonable moisture and pH value, and brings convenience to crop absorption and utilization; the preparation technique is simple, has low production cost, and is easy to exert; and the active phosphate fertilizer has the characteristics of soil looseness, increment of granular structures and fertility improvement, and is the high-quality fertilizer in the non-hazardous agriculture.