The invention discloses a method for preparing Rebaudioside E through an enzyme method. By means of the method, through tomato source UDP-glycosyl transferase and potato source sucrose synthetase, with stevioside as the raw material, the Rebaudioside E is produced through one-step glycosylation; meanwhile, by means of the fixed-point mutation technology, the UDP-glycosyl transferase is transformed, and the yield of the Rebaudioside E is further improved. By means of the method, no UDP-glucose or UDP needs to be added, the UDP-glucose is obtained as the raw material of glycosylation under the sucrose synthetase decomposition effect of the UDP in a crude extraction solution and the added sucrose, a double-enzyme circulating reaction system is established, and the stevioside is effectively catalyzed to generate the Rebaudioside E. The yield of the Rebaudioside E can reach 65% or above; through the fixed-point mutation technology in the later period, N358F beneficial mutants are obtained through screening, and the yield of the Rebaudioside E is improved through the catalysis and can reach 85% or above at most. Compared with an existing Rebaudioside E preparing method, the method is simple in processing step, low in cost and high in yield and has important application value.