This paper investigates the synergetic control strategy for water hammer wave and mass wave in hydropower station with downstream channel. Firstly, the mathematical model of hydropower station with downstream channel (HSDC) and hydropower station with downstream channel and surge tank (HSDCST) are established. Then, the controller formula of HSDC and HSDCST are derived on the basis of the synergetic theory. Furthermore, it is parsed that the dynamic characteristics of HSDC and HSDCST to various disturbances under synergetic control strategy. Finally, the robustness and applicability of synergetic control strategy for HSDC and HSDCST are analyzed. The results indicate that the macro variable is the linear combination of state variables and their derivatives based on feedback linearization of the state equation. For the hydropower station under the synergetic control strategy, it has excellent dynamic characteristics employing sensitive response, small overshoot, fast attenuation speed and no static error. The synergetic control strategy is superior to the PID control strategy under various disturbances in controlling the amplitude of water hammer wave in HSDC, which is down 12.5%. The attenuation of mass wave in HSDCST under synergetic control strategy is faster, and the settling time is 6.16s less than that of PID control strategy. The synergetic control strategy is superior to the PID control strategy under various disturbances in controlling the amplitude of water hammer wave in HSDC and the attenuation of mass wave in HSDCST. Compared with PID control strategy, it is the robustness of synergetic control strategy that are much more advantageous for HSDC and HSDCST. Specifically, RI value is about 1.65, 0.18 for HSDC and 2.21, 0.25 for HSDCST under synergetic control strategy, while it is about 3.05, 1.20 and 3.32, 1.30 under PID control strategy. Moreover, the synergetic control strategy has a wide applicability in controlling the water hammer wave in HSDC and mass wave in HSDCST.