Aiming at the special environment of the air-breathing hypersonic ramjet flight test, especially the booster separation conditions, the multi-body separation of an axisymmetric hypersonic aircraft was studied. Six degrees of freedom solver and local mesh reconstruction based on non-structured mesh method were proposed to simulate the separation process. Results include motion parameters of the booster and the aerodynamic characteristics ranging from 0 ms to 300 ms for the aircraft under the weak perturbance states. Meanwhile, the trajectory curve of separation was demonstrated. Finally, the feasibility of the subsequent scheme was estimated and the optimal conditions for the separation reached requirement of mild interference.