Abstract: The structural instabilities of base flow are presented by using numerical simulation in this paper in hypersonic base flow over blunt cone with M_∞ =6, Re=1.71× 10⁶(based on the nose radius) and Apollo command module with M_∞ =6, Re=1.71 × 10⁶(based on the nose radius). Stable solutions are first obtained to show a primary separation and a secondary separation zone in flow over blunt body at M_∞ =6. Later, without any arbitrary disturbance imposed, the structural instability still occurs after a certain critical time. The evolving process of the structure of flow over blunt body is a periodic behavior in the forepart, but there is non-periodic behavior observed at M_∞ =6 in spite of long calculation time. For Apollo command module, the simulation result is similar to that of the blunt body, while the base flow of Apollo command is more instability than that of blunt cone. This research indicates that the present numerical simulation method can be used for the study of the stability of base flow.