The invention discloses a preparation method of a biological organic fertilizer for improving the fresh juice quality of Fuji apples. The method comprises the following steps: 1, preparing a fish scale enzymatic hydrolysis broth; 2, preparing a fermented rice straw material; 3, preparing a fermented cow and sheep dung material; 4, mixing the fish scale enzymatic hydrolysis broth, the fermented rice straw material and the fermented cow and sheep dung material, inoculating an EM inoculant, and carrying out secondary fermentation; and 5, air-drying, crushing, and carrying out bagging preservation. The biological organic fertilizer obtained through respective fermentation of various organic raw materials, mixing and secondary fermentation is rich in highly active amino acids, proteins, various micro and trace elements and beneficial microbes, can meet the growth demands of Fuji apples, improves the output and quality, improves the soil quality, especially improves the fresh juice quality of the Fuji apples, delays the browning speed of the juice, improves the mouthfeel quality, facilitates application of the Fuji applies in the field of fresh fruit juices, and has wide popularization values.