The existence of a shared pipeline in a multi-machine system can lead to hydraulic coupling effects between units. It increases the difficulty of controlling hydroelectric units and affects the stability of the power system. This paper refines the model of the hydroelectric generator unit and builds a nonlinear model of a hydro-generator unit with the single penstock multi-machine system. The synergetic control theory was introduced, and the governor and excitation system controllers were designed separately. A joint synergistic controller is obtained by analyzing the two systems' synergistic factors and controlled characteristics. This controller realizes the joint control of the excitation and governor system. The simulation selected a proportion-integral-derivative (PID) controller with optimized parameters, synergistic governor controller (SEC), and synergistic excitation controller (SGC) for comparison to verify the effectiveness of the proposed method. The results indicate that the proposed control method exhibits competent control effects in the single penstock multi-machine system. It can reduce the impact of hydraulic coupling, shorten the adjusting time, and ensure the fast and stable operation of the system. In addition, the values of system time parameters and synergetic control parameters are analyzed separately to provide a reference for achieving optimal control.