This paper investigates the integrated control of an air-breathing hypersonic vehicle considering the safety of propulsion system under acceleration. First, the vehicle/engine coupling model that contains a control-oriented vehicle model and a quasi-one-dimensional dual-mode scramjet model is established. Next, the coupling process of the integrated control system is introduced in detail. Based on the coupling model, the integrated control framework is studied and an integrated control system including acceleration command generator, vehicle attitude control loop and engine multivariable control loop is discussed. Then, the effectiveness and superiority of the integrated control system are verified through the comparison of normal case and limiting case of an air-breathing hypersonic scramjet coupling model. Finally, the main results show that under normal acceleration case and limiting acceleration case, the integrated control system can track the altitude and speed of the vehicle extremely well and adjust the angle deflection of elevator to offset the thrust moment to maintain the attitude stability of the vehicle, while assigning the two-stage fuel equivalent ratio to meet the thrust performance and safety margin of the engine. Meanwhile, the high-acceleration requirement of the air-breathing hypersonic vehicle makes the propulsion system operating closer to the extreme dangerous conditions. The above contents demonstrate that considering the propulsion system safety will make integrated control system more real and meaningful.