In order to study the influence of separator diaphragm on pulse solid rocket motor, simulation model was presented. Based on three types of separator diaphragms, the 3-D flow field through pulse solid rocket motor was simulated when the motor working on the second and the third pulse, and physical parameter distribution in inner flow filed was obtained and certificated by confirmatory tests. At last, the influences of the patterns and size of the holes imposed on ablative shielding of combustion chamber and separator diaphragm ware analyzed, the countermeasures were offered. The conclusions of this paper can serve as references for optimal design of separator diaphragm.