The integration of the pumping station between conventional cascade hydropower stations to form the hybrid pumped storage has the potential to increase the hydropower’s flexibility and promote the consumption of renewable energy into the power grid. However, the conversion of electricity and water potential energy between the pumping station, hydropower, wind power, and photovoltaic poses challenges to the operation of the multi-energy sources. This study explores the complementary operation of the hybrid pumped storage-wind-photovoltaic system at different time scales and evaluates the economic benefits and energy efficiency of the system. First, a multi-scale nested joint operation model that considers both long-term and short-term operation strategies is proposed to simulate the operation process of the hybrid system. Then different operation strategies are set considering the operation time scale of the pumping station. The case study in the Wujiang River, China, demonstrates that the hybrid pumped storage can increase power generation profit and decrease energy curtailment, and consideration of long-term scale and short-term scale nested operation can further increase the system’s profit. The pumping station can increase the amount of available water during the dry season on a long-term scale and store excess electricity from renewables and the grid on a short-term scale. The benefits of hybrid pumped storage are further validated under different reservoir inflows and electricity prices.