Due to the existence of hydraulic coupling in the single penstock multi-machine system, the stability time of the unit is prolonged when power disturbance occurs, which is not conducive to the stability of the power system. Based on the synergy theory, this paper builds a nonlinear model of a hydro generator unit with the single penstock two-machine system, adds the synergy factors of the governing system and the excitation system, describes the characteristics of the controlled system, and derives the control law. A simulation system is built to verify the effectiveness of the proposed method. Load disturbance and three-phase short-circuit fault are set up to compare the dynamic response effects of the PID controller with optimized parameters and the synergetic controller. The results show that the proposed control method has a better control effect in the single penstock two-machine system and can better reduce the influence of the common pipe due to hydraulic coupling, shorten the stabilization time, and ensure the stability of the system. In addition, the values of regulation and synergetic control parameters are analyzed separately to provide a reference for achieving better control.