The process of separating stages is crucial for multistage rockets, directly influencing the success of the launch plan. Different separation timing methods alter the flow field structure within the interlevel zone at separation, influencing the separation of the two-stage rockets. This paper employs the SST k-ω turbulence model to investigate the structure of the flow field and its aerodynamic and motion characteristics under different nozzle baffle opening and separation times, taking into account variable properties, supersonic compressibility, and the upstream–downstream interference. First, we examined the standard flow field structure, considering the engine jet, the lateral jet between stages, and the disturbance from the external supersonic inflow. Then, we discussed the displacement characteristics and axial force coefficient curves of the first and second steps of the separation process. Finally, we explored the impact of baffle opening and separation times on the flow field structure and axial force coefficients of the two stages at the onset of separation. For the flow field structure, a delay in the baffle opening and separation moment led to a gradual increase in downstream and separation regions until they stabilized after a certain range. However, the axial force coefficients displayed different behavior before and after the design point.