In this article, a new power system based on the Stirling engine and hydraulic free piston engine is proposed to provide power for reverse osmosis (RO) desalination. First, the design of the Stirling free piston RO desalination power system was carried out, and the size parameters of the main structures such as the regenerator, heater, cooler, power piston, and valve distribution piston were obtained. A physical model was established to simulate the process of the Stirling engine driving the RO desalination power system based on finite element CFD. The flow field distribution cloud map and output power of the Stirling engine were analyzed. The results indicate that the gas motion of the Stirling engine is stable, and the entire power system can operate normally.