Hybrid step motor is one of the primary candidates for direct drive motor due to its high torque and low speed, but the vibration it produces is a major drawback to use it in applications. The micro-step method is typically used to reduce the vibration and to obtain high resolution motor steps, which divides a single step into many micro-steps. PWM (Pulse Width Modulation) is the most common method to control the micro-step motor, but the equivalent magnetic circuit taking into account the localized saturation throughout the hybrid step motor is a non-linear model. This paper presents the development of a non-linear FPGA based driver for controlling five-phase hybrid step motor. The application circuit we developed is aimed for use in a low cost system. Simulations were done, and circuit analysis tests were carried out to verify our design, using prototype circuit boards. Low vibration and high resolution steps are achieved by using our nonlinear micro-step control method.