The invention relates to a method for preparing cephalosporin through enzyme catalytic acylation. The method comprises the steps of A, performing an acylation reaction: performing the acylation reaction of an acylation reagent and beta-lactam in the presence of a catalytic enzyme to obtain product slurry; B, performing shaking separation: controlling the viscosity of the product slurry and performing the shaking separation on the product slurry under a certain process condition by adopting a shaking screen to obtain catalytic enzyme filter residues and a cephalosporin suspension filter liquor; and C, performing product refining: filtering the cephalosporin suspension filter liquor to obtain cephalosporin wet powder, and performing washing and drying to obtain a refined product. According to the method, a technological process and technological parameters are optimized, so that the problems of difficulty in enzyme separation, high preparation cost, serious environmental pollution and the like in an existing process are solved, and while the product quality can be ensured, the technological process is simplified, the separation efficiency and the production efficiency are improved, and the production cost is reduced.