A large amount of redundant energy gained from incident solar energy is dissipated into the environment in the form of low-grade heat, which significantly reduces and limits the performance of photovoltaic cells, so removing or storing redundant heat and converting it back into available thermal energy is a promising way to improve the utilization of solar energy. A new combined water-based solar photovoltaic-thermophotovoltaic system embedded in the phase change material (PCM) mainly is proposed and designed. The effects of the water flow rate, cell operating temperature, the presence of PCM, and the thickness of the PCM factor on the overall module performance are explored comprehensively. The maximum thermal power output and the corresponding efficiency of the combined-system-embedded PCM are calculated numerically, The results obtained are compared with those of the PV (photovoltaic) and PVT(photovoltaic-thermal) cells with the same solar operating conditions. In addition, the PVT-PCM system possesses a higher power output and overall efficiency in comparison with the PVT and PV system, and the maximum cell temperature reduction of 12.54 °C and 42.28 °C is observed compared with PVT and PV systems. Moreover, an increased average power of 1.13 W and 4.59 in PVT-PCM systems is obtained compared with the PVT system and the PV system. Numerical calculation results illustrate that the maximum power output density and efficiency of the PVT-PCM are 3.06% and 16.15% greater than those of a single PVT system and PV system in the working time range, respectively. The obtained findings show the effectiveness of using PCM to improve power output and overall efficiency.