With the rapid development of renewable energy, the integration of multiple power sources into combined power generation systems has emerged as an efficient approach for the energy utilization. Pumped storage power stations, as large-capacity flexible energy storage equipment, play a crucial role in peak load shifting, valley filling, and the promotion of new energy consumption. This study focuses on the combined pumped storage-wind-photovoltaic-thermal generation system and addresses the challenges posed by fluctuating output of wind and photovoltaic sources. First, a K-means clustering analysis technology has been introduced to identify the typical daily scene output and load fluctuation patterns in an energy base in northwest China. Based on the operation constraints of each subsystem, aiming at the optimal comprehensive benefit, minimum generalized load fluctuation, and minimum carbon emission, an operation optimization scheduling model for the pumped storage-wind-photovoltaic-thermal combined power generation system has been established. When the optimization model has a configuration scale of 3000 MW for wind power and 2800 MW for photovoltaics, the pumped storage power station in the combined power generation system can achieve full pumping for 4 h and full generation for 5 h, which plays an obvious role in peak and valley regulation. Meanwhile, the combined system minimizes operating costs and carbon emissions, resulting in a minimum fluctuation of thermal power output by 6.6%. Furthermore, different capacity configurations demonstrate a non-linear relationship between the comprehensive benefits, carbon emissions, and the scene penetration rate. When prioritizing economic stability over carbon emissions, a thermal power capacity configuration of 7200 MW leads to the lowest total operating cost for the combined system, amounting to 26.38 million ¥. Results indicate that pumped storage effectively suppresses grid power fluctuations, promotes the consumption of renewable energy sources, and enhances the stability of thermal power output.