A motion controller was designed to achieve stable running of a four-stroke free-piston linear generator. Simulation model of the free-piston motion controller was built based on the control theory of hybrid system. Motion control process was analyzed by using the proposed model and the model of a free-piston linear generator. Effects of circulation burning fluctuations and misfires were discussed. Based on the results of the simulation, an electronic control system was designed by using a high-performance digital signal processor. Testing results of the electronic control system were analyzed in detail. According to the simulated and tested results, the designed motion controller has the advantages of simplicity and reliability. It satisfies the requirement of four-stroke free-piston linear generator for piston motion control.