To prevent scramjet inlet unstart, stringent control over the shock train's leading edge in the isolator is necessary. Therefore, this study proposes a fuel flow active control scheme combining an adaptive particle swarm optimization algorithm (APSO) and active disturbance rejection control (ADRC) to enhance the traditional control (such as proportional-integral-derivative, PID) system's stability and anti-interference capabilities in complex and uncertain environments. Within this context, a simple, semi-empirical mathematical model of a dual-mode scramjet is constructed. An ADRC controller is designed to counteract the nonlinearity and disturbance of the dual-mode scramjet. ADRC, not requiring an accurate mathematical model, utilizes its extended state observer to estimate all uncertain factors affecting the controlled object based on the relationship between the shock train's leading edge and the controller's output, treating them as unknown disturbances for compensation, thereby exhibiting strong anti-interference capabilities. In order to optimize the performance, the APSO is introduced to fine-tune the ADRC controller parameters. The APSO reduces the rise time of ADRC from 22.28 to 11.39 ms, and the adjustment time from 40.05 to 13.64 ms. The APSO effectively tunes the parameters of the ADRC controller, which ensures rapidity comparable to the PID and all-coefficient adaptive control (ACAC) in managing the shock train's leading edge. At the same time, ADRC has stronger anti-interference ability and adaptive ability than ACAC and PID. This research preliminarily verifies the feasibility and advancement of the ADRC for shock train leading-edge control in scramjet isolators.