The invention provides a lipase-calcium phosphate compound enzyme crystal, a preparation method thereof and a method for catalyzing and synthesizing clindamycin palmitate by using the lipase-calcium phosphate compound enzyme crystal, and belongs to the technical field of antibiotic drug synthesis. According to the method, clindamycin free alkali shown in the formula I and ethenyl hexadecanoate shown in the formula II serve as a substrate and react with a reaction solvent for 6-30 h at the temperature of 30-80 DEG C under the catalytic function of the lipase-calcium phosphate compound enzyme crystal, and clindamycin palmitate shown in the formula III is prepared. The lipase-calcium phosphate compound enzyme crystal prepared through the method is a calcium phosphate crystal of thermomyces lanuginosus lipase. The lipase-calcium phosphate compound enzyme crystal has the advantages that the cost of the method is low, immobilized enzyme cannot be dissolved in an organic solvent and can be recycled, the yield can reach 75.8% at most, the method is safe, reliable, low in environment pollution and suitable for industrial production.