Due to the free piston engine alternator potential advantages in terms of fuel efficiency, a magnetic dynamic model was developed to describe the dynamic characteristics of free piston alternator as the Hybrid Electric Vehicle power source. The mathematic model for the permanent magnet linear alternator was introduced. A function was designed to descript the relation between the individual coil fluxes and the mover motion. And then, the total system model was simulated, and extensive simulation results are presented, giving insight into the free piston alternator operating characteristics and performance. The free piston alternator performances based on the mathematical model were also discussed comparing with prototype experiments.