The invention discloses a special fertilizer for fruit trees and a preparation method thereof. The fertilizer comprises a base fertilizer and a leaf fertilizer, wherein the base fertilizer is prepared from the following raw materials: an organic fertilizer, urea, monoammonium phosphate and potassium chloride, the organic fertilizer is prepared by fermenting raw materials, namely dry chicken manure, cornstalk, rice husk, fruit tree leaves, bean cakes and needle mushroom dregs by virtue of complex microbial inoculants, and the leaf fertilizer comprises the following components: urea, monopotassium phosphate, farm-oriented chitosan oligosaccharide, 6-BA, multi-effect triazole, triazolone, polyethylene glycol 200, sodium tetraborate and microelements. The fermented organic fertilizer not only contains a large quantity of beneficial bacterium, organic matters and multiple microelements, but also can be used for increasing the beneficial bacterium of the soil, fix nitrogen, dissolve phosphorus, activating the soil after being applied, improving the water retentivity, fertilizer using efficiency and fertilizer persistent effect of the soil, and achieving the effect of a controlled-release fertilizer; in addition, the leaf fertilizer is applied in different growing stages of the fruit trees, thus supplementing nitrogen, phosphorus, potassium and microelements, promoting to bear and expand fruits, and improving the stress resistance of the fruit trees.