The effect of chymopapain autolysis on its purification was studied. It was found that: activated and inactivated chymopapain solution could undergo autolysis. The use of activator accelerated the autolytic process, resulting in heterogeneity of the purified products, and decline in the recovery of enzyme activity and protein. By contrast, using inactivated chymopapain inhibited or delayed the autolysis, the recovery of protein was 64.08%, showing an increase of more than 10%, and recovery of activity was 68.9%, a gain of over 15%.