Abstract: There are some problems of return capsule during reentry process, such as high heat flux of shoulder, prediction of base drag and unsteady vibration. Solve these problems, the key is accurate identification of separation and transition physical phenomenon. In this paper, separation and transition phenomenon of return capsule during reentry process under high Reynolds number condition are investigated by means of large eddy simulation (LES), base flow patterns and stability characteristics of return capsule are obtained. Physical mechanisms of base flow instability are analyzed from the aspects of shoulder shear instability, base flow structure instability and wake region instability. The results show that base flow stability of return capsule all includes shoulder shear instability mode and base flow structure instability mode, there is interaction between the two instability modes, there is are oscillation characteristics of Karman vortex street in the far wake turbulent region. These understandings support mechanism of the effect of external disturbances on the base region and stability control of return capsule in the theory.