Abstract: To compare the inactivation effect of different treatments on anti-nutritional factors, thermal treatment, microwave treatment, lye soaking, dehulling and other processing measures were applied. The result indicated that a thermal treatment at 88℃ for 10min reduced the lipoxygenase activity to 14.20%, while a thermal treatment at 100℃ for 20min reduced the trypsin inhibitors activity to 9.96%. Treated by microwave cooking (2450MHz, 800W) for 2min, lipoxygenase activity was reduced to 8.86%, and a microwave cooking (2450MHz, 800W) for 8min and 4min reduced the trypsin inhibitor activity and urease actirity to 11.24% and 1% respectively. Compared to conventional thermal treatment, microwave cooking inactivated anti-nutritional factors more quickly, shortening the processing time. In addition, processing steps like soaking in 0.5% NaHCO3 solution and dehulling contributed to the inactivation of anti-nutritional factors, and could be utilized combining with heat treatment and microwave treatment to reduce soymilk processing time.