A superconducting Maglev system suspended by EDS intrinsically has negative magnetic damping. In order to improve the magnetic damping, we used a linear generator by controlling the power factor of the current in the linear generator coils. We developed a PWM converter and a simulator (using Micro Cap V) for this control. This paper describes how to control the PWM converter and subsequently the power factor, and the result of confirmation of this control method through simulation and synthetic bench tests. We can now control the PWM converter and the power factor without a effecting the output power.