Sodium alginate embedding method and chitosan crosslinking method were used to immobilize α -galactosidase from Clitocybe squamulosa. The optimum pH, pH stability, optimum temperature, temperature stability, storage time of immobilized enzyme and free enzyme were compared. The hydrolysis on oligosaccharides in soymilk and operational stability of the two immobilized enzymes are compared. The results showed that the optimal saturation of ammonium sulfate was 80% for α-galactosidase from C. squamulosa. The enzyme activity retention rates of the two immobilized methods were both more than 50%, and the temperature stability, pH stability and storage time of immobilized enzyme were improved compared with that of free enzyme. After comparing the two immobilized enzymes, the temperature, acidity stability and operation stability of chitosan immobilized enzyme were better than that of sodium alginate immobilized enzyme. But the hydrolysis efficiency of chitosan immobilized enzyme on soymilk oligosaccharide was lower than the latter. The hydrolysis rate of oligosaccharide was more than 85% after the two immobilized enzymes were reused for 3 times. Compared with sodium alginate, chitosan was more suitable to be the immobilized carrier of α -galactosidase from C. squamulosa.