The free-piston hybrid power system (FPHS) is affected by the dynamic coupling of combustion drive, power transmission, piston motion, excitation generation and gas exchange, and its operating state is very different from that of traditional engines. In this paper, the influence of the change of electromagnetic load on the ventilation stability of the whole system is studied by combining the method of system simulation and experimental validation. A dynamic-ventilation one-dimensional coupled gas exchange model was established, and the influence of the fluctuation of the electromagnetic load on the gas exchange is simulated by combining the thermodynamic model with the magnetic inductive load model. The results show that the scavenging efficiency is positively correlated with the load fluctuation, while the trapping efficiency changes with the opposite rule. Specifically, increasing the electromagnetic load properly will increase the time of gas exchange and obtain more fresh charge. The reduction of the electromagnetic load will make the compression process have higher gas pressure and temperature, which the mixture of oil and gas is more homogeneous and the combustion rate is faster after ignition. The stability of the ventilation performance of FPHS is very sensitive to electromagnetic fluctuations. The control of FPHS system can be achieved by adjusting the electromagnetic load.