In this paper, we propose a novel method for frame-by-frame intermittent tracking to facilitate motion-blur-free video and resolve the tradeoff between brightness and motion blur when shooting moving objects by vision sensor. With the proposed method, vision-based tracking is performed when the shutter is open, and back-to-home control is performed when it is closed. This process occurs at dozens or hundreds of frames per second. We develop a prototype motion-blur-free microscope by implementing our frame-by-frame intermittent tracking method on a piezo-actuator-based microscopic tracking system, accelerated by a high-speed vision platform. Our motion-blur-free microscope can capture non-blurred 512 × 512 images at 125 fps with frame-by-frame intermittent tracking and its performance is verified by showing the experimental results from several moving scenes in microscopic view.