A PID-self-impedance fault-tolerant controller based on the inner and outer loop structure is developed for a new form of bi-rotor vehicle, taking into account the fault-tolerant control problem when the actuator fails. First, the dynamics model and actuator fault model of the bi-rotor vehicle are established, the PID active fault-tolerant controller with control parameter switching is selected for the outer loop, and the self-immune controller is selected for the inner loop. Second, when a fault occurs, the outer loop PID controller’s settings are switched to the controller parameters of the relevant fault state based on the extent of the fault, and the parameters are matched with the robust controller of the inner loop to achieve fault-tolerant control. Finally, simulation experiments show that the designed fault-tolerant controller can still achieve stable tracking of position and attitude in the presence of actuator faults. This indicates that the flight control system is robust to fault-induced disturbances and effectively improves the vehicle’s fault-tolerant performance.