Under supersonic state, the aero-propulsion system exhibits different coupled characters in deceleration from that in acceleration. However, the deceleration control has not been fully studied. In order to solve the coupled problems, an integrated component-level model including inlet and turbofan engine was established. Based on the integrated model, the particularity of inlet adjustment during deceleration was analyzed. And the analyzed results showed that the inlet regulation is not necessary to keep the inlet and engine working in well-matched at any time under supersonic state. Due to the coupled relationship between inlet and turbofan engine, a new optimal integrated control scheme is proposed in this paper. The inlet ramp angle is taken as an optimal control variable as the same as main fuel mass flow and nozzle throat area. The simulation results indicate that inlet ramp angle regulation showed a more effective control quality in the rapid drop of aero-propulsion–installed thrust. Furthermore, the deceleration could be completed in a shorter control time.