[Objective] In response to the operational challenge caused by high penetration of wind and solar power in modern power systems, this study aims to propose a bi-level optimized scheduling model for a multi-energy complementary power generation system incorporating pumped storage. The model seeks to enhance renewable energy utilization, optimize system economic performance, and improve system stability. The novelty lies in the integration of a bi-level optimization framework with a deep peak shaving strategy, while introducing CO₂ emission intensity and thermal power output coefficient as evaluation indicators for multi-objective coordination of economy, environmental performance, and stability. [Methods] The upper-level model optimized the joint dispatch of wind, solar, hydro, and pumped storage with objectives of maximizing wind and solar output, minimizing net load fluctuation, and minimizing curtailed electricity. The lower-level model optimized the economic performance of the system, aiming at minimizing thermal power operational costs, pumped storage costs, and curtailed electricity penalties. Constraints included wind and solar output limits, hydro and pumped storage capacity limits, thermal unit ramping capabilities, and power balance requirements. The CPLEX solver combined with the YALMIP toolbox was employed to solve the high-dimensional nonlinear mixed-integer programming problem. CO₂ emission intensity and thermal power output fluctuation coefficient were adopted as additional evaluation metrics to quantify environmental performance and system stability. [Results] Simulation results indicated that integrating pumped storage reduced total cost by 46 000 CNY (1.02%) and CO₂ emission intensity by 6.4% in the summer scenario, while the thermal power output fluctuation coefficient decreased from 33.34% to 7.88%. In winter, thermal output stability improved to 7.67%. Increasing wind-solar penetration from 31.25% to 47.62% lowered system costs by 39.5% and reduced CO₂ emission intensity by 58.3%. Enhancing deep peak shaving from 50% to 70% reduced total cost by 19.2% and decreased thermal power output fluctuation coefficient by 44.2%. [Conclusions] The introduction of pumped storage power station significantly enhances system flexibility, increasing renewable energy utilization by over 12% and reducing thermal unit peak regulation pressure by 50%. The bi-level optimization model ensures low-cost operation while reducing CO₂ emission intensity by more than 0.1 kg/kWh and maintaining thermal power output fluctuation coefficient below 8%. A combination of high wind-solar penetration (>40%) and deep peak shaving (70%) achieves optimal comprehensive benefits, providing theoretical support for scheduling of high renewable energy penetration power systems. This study provides an innovative methodology for the design and optimization of wind-solar-hydro-thermal-pumped storage multi-energy systems, and the findings can be generalized to other clean energy bases.