The invention discloses an efficient functional fertilizer and a preparation method thereof. The efficient functional fertilizer is obtained by mixing and fermenting raw materials, including composition A and composition B, in certain parts by weight, wherein the composition A comprises urea, cellulose, bean cake, carbon black, polypropylene glycol, monoammonium phosphate, calcium superphosphate, potassium sulphate, potassium chloride, palygorskite, zinc sulphate, ferrous sulphate and nitrogen-fixing bacteria fertilizer; and the composition B comprises organic waste, hydroxypropyl methacrylate, ethyl acetate, ammonium acrylate, river sand, calcium powder, bone powder, ammonium molybdate, trace element fertilizer, kaolin and potassium silicate fertilizer. The preparation method is simple, the prepared efficient functional fertilizer can effectively provide lodging resistance, disease resistance and drought resistance for crops, absorption rate of the crop is high, utilization rate of the fertilizer is improved, and harm to soil is correspondingly reduced to some extent.