A novel photovoltaic-thermal system combining phase change materials and water cooling is proposed to cool photovoltaic panels and enhance overall performance. Based on experimental results, the thickness of the phase change material and the optimal flow rate are optimized using the control variable method. First, photovoltaic modules with and without water cooling are tested by varying the flow rate. At a mass flow rate of 0.023 kg/s, the thermal efficiency reached 45.83 %, electrical efficiency is 10.5 %, and comprehensive efficiency is 57.81 %. Comparison of these efficiencies with those at other flow rates indicates that the thermal, electrical, and comprehensive efficiencies are all superior at this flow rate. As a result, 0.023 kg/s is determined to be the optimal flow rate. Second, three-dimensional modeling and simulations are conducted, and the simulation results are compared with experimental data to verify the model's accuracy. The control variable method is used to analyze the impact of different phase change material thicknesses on system performance at the optimal cooling flow rate. Simulation results showed that at a phase change material thickness of 0.03 m, the photovoltaic efficiency reached 11.98 %, and overall efficiency reached 63.33 %, higher than those at other thicknesses. Compared to photovoltaic-thermal systems without phase change material, the proposed system demonstrated superior performance. The system significantly enhances photovoltaic utilization and waste heat storage.