Separation flow could be generated in a high-altitude nozzle, in order to study the flow separation on the nozzle performance. A three-dimensional numerical simulation about the separation flow in the high-altitude nozzle of a solid rocket motor (SRM) was conducted. The flow results with different inlet total pressure were obtained by utilizing CFX software. It shows that, due to the separation flow, there are some adverse effects for the stability and thermal protection of the nozzle. The simulation provides a reference of the design of the high-altitude nozzle, also a basis for further study.