Based on Computational Fluid Dynamic technology, the mixing process of Rocket Based Combined Cycle (RBCC) propulsion system is researched. The idea of RBCC propulsion system means combining rocket engine with ramjet engine effectively, which can flight from sea level to high altitude in wide Mach ranges. In order to analyze how the length of the mixing part affects mixing process, different length of mixing part are researched. As it is indicated, with a constant Mach number, increasing the length of mixing part makes main flow and second flow mix more evenly. Moreover, the length of mixing part has a slight impact on the thrust. Obviously the main consequence of increasing the length of mixing part is promoting the mix of main flow and second flow. Therefore, in order to decrease the weight of aircraft, it is of importance to reduce the length. Through comparing distribution of different cases, when working in the situation of maximum power, the flow in the nozzle of rocket engine is under expansion, while that in the nozzle is fully expanded. Nevertheless, in the case of high altitude and high Mach number, there exists a vortex in the nozzle of rocket engine because of over expansion; meanwhile, the flow in the nozzle is under expansion. Therefore, it is necessary to adjust nozzle throat area in order to increase the thrust of RBCC at high altitude.