The invention relates to a preparation method of a compound fertilizer dedicated to ginkgo trees, in particular to a preparation method of the compound fertilizer dedicated to ginkgo trees by using blue-green algae as a base material, belonging to the technical field of fertilizers. The preparation method comprises the steps of squeezing blue-green algae to remove excessive moisture to obtain wet blue-green algae, sequentially adding water, cellulase and protease in parts by weight, mixing uniformly, heating, carrying out enzymolysis, and performing enzyme deactivation to obtain enzymatic hydrolysate; adding potassium sulphate in the enzymatic hydrolysate, heating, keeping the temperature for 3-5h, cooling, and carrying out vacuum concentration to obtain concentrated solution; adding sodium humate, potassium humate, ammonium bicarbonate, phosphogypsum, potassium citrate, zinc sulfate, amino acid, polyvinyl alcohol, cellulose and calcium carbide in the concentrated solution, stirring uniformly, spray-drying, and then granulating to obtain a product. The compound fertilizer dedicated to the ginkgo trees can enable the ginkgo trees to have higher stems and more leaves and have high content of active substances.