The invention discloses a special amino acid water-soluble fertilizer for lemons and a preparation method thereof. The special amino acid water-soluble fertilizer for lemons is composed of urea, monoammonium phosphate, ammonium sulfate, potassium nitrate, all-water-soluble humic acid, borax, white vitriol, magnesium sulfate monohydrate and EDTA iron chelate. The preparation method comprises the following steps: respectively pulverizing the urea, monoammonium phosphate, ammonium sulfate and potassium nitrate, carrying out humidification and heating to perform aggregation granulation and mixing to obtain a material A, pulverizing the all-water-soluble humic acid, borax, white vitriol, magnesium sulfate monohydrate and EDTA iron chelate, and uniformly mixing to obtain a material B; and uniformly mixing the materials A and B, granulating, drying, screening and cooling. The special amino acid water-soluble fertilizer for lemons can keep the nutrition balanced in the young lemon tree vegetative growth period and fruit swelling period, enables the lemons to quickly and effectively acquire required nutrients, ensures the healthy development and growth of the trees and fruits, enhances the crown establishment and fruit yield and improves the quality.