The invention belongs to the field of agriculture, and particularly relates to a fruit tree organic fertilizer and a preparation method thereof. The fruit tree organic fertilizer is prepared from thoroughly decomposed livestock excrement, bagasse, forchlorfenuron, leaf mold, traditional Chinese medicine extraction residue, potassium chloride, urea, fishbone dust, chelated iron, calcium superphosphate, zinc chloride, diammonium phosphate, copper sulphate, lignin, urea phosphate, paclobutrazol, cellulose, borax, attapulgite, chitosan and chitosan oligosaccharide. The fruit tree organic fertilizer and the preparation method provided by the invention have the advantages that the medicinal value of the medicine slag is sufficiently utilized; the plant diseases and insect pests of crops can be reduced; the pesticide consumption is reduced; the ecological environment is protected; the nutrition substances are provided for the plants through organic fertilizers; the slow-release fertilizer is prepared; the absorption rate of phosphorus and potassium in the soil is effectively improved, so that the consumption of organic and inorganic compound fertilizers is reduced; the utilization rate of the fertilizer is improved.