Abstract: The whole cells of Aspergillus niger with high yield of fructosyltransferase were immobilized by using the embedding method. Then, the sodium alginate-chitosan was used as the carrier, and the optimum immobilization conditions were obtained by using the single factor and orthogonal experiment optimization, respectively. The single-factor optimization test results showed that: the optimal concentration of sodium alginate was 2%, the optimal quantity of bacteria embedded was 150 g·L⁻¹, and the optimal concentrations of chitosan and CaCl₂ were both 4%. The results of orthogonal test showed that when the concentration of sodium alginate was 3%, the quantity of bacteria embedded was 200 g·L⁻¹, the concentration of chitosan was 5%, and the concentration of CaCl₂ was 3%, the recovery of enzyme activity could reach the optimal 74.7%. The validation test showed that the immobilized cells were catalyzed for the synthesis of fructooligosaccharides in seven consecutive batches, and still had 96.85% residual activity, which had good potential for application and provided a new technical route for the synthesis of fructooligosaccharides.