Speed, accuracy and smoothness are the important properties of pan-tilt camera. In the case of a high ratio zoom lens system, low vibration characteristic is a crucial point in driving pan-tilt mechanism. In this paper, a novel micro-stepping controller with a function of reducing vibration was designed using field programmable gate arrays (FPGA) technology for high zoom ratio pan-tilt camera. The proposed variable reference current (VRC) control scheme reduces vibration decently and optimizing coil current in order to prevent the step motor from occurring missing steps. By employing VRC control scheme, the vibration in low speed could be significantly minimized. The proposed controller can also make very high speed of 378kpps micro-step driving, and increase maximum acceleration in motion profiles.