Owing to the influence of uncontrollable factors (e.g., climate), wind and photovoltaic (PV) energy are highly fluctuating and undispatchable, thereby hindering their integration to the grid. To address this issue, complementary systems using hydropower as a regulating energy are gradually emerging. With the development of wind and PV power industries and the electricity spot market, wind and PV power subsidies are being reduced, and the bidding subjects are diverse. It is likely that wind, PV, and hydropower will participate in the market with the same quality and price. Wind–photovoltaic–hydropower complementary systems (WPHCSs) normally aim at minimum wind and PV power curtailment, which do not consider hydropower production aspects. This study considers the effect of complementary operation on hydropower in the context of energy indifference bidding in the future electricity spot market, establishes a comprehensive benefit index system to optimize WPHCS, and proposes a particle swarm optimization algorithm that introduces the dominant solution with an adjustable parameter to solve the maximizing comprehensive benefits of a complementary system model. Control experiments with different loads, storage capacities, inflows, and models were conducted to verify the superiority of the proposed model and to summarize the optimal operation rule of the complementary system. The results show that turbine efficiency is the main factor affecting the results, and the total benefit of the system could be improved by up to 69% comparing with the priority consumption of wind and the PV power model. This paper describes the WPHCS benefits more comprehensively, and the results can be used to improve the benefits of complementary systems.