We develop a motion-blur-free microscope for shooting non-blurred videos of moving objects by implementing a frame-by-frame intermittent tracking method with a microscopic high-speed tracking system that controls the position of the objective lens using high-frame-rate video processing. With our tracking method, the control target alternates at several hundred hertz, according to the camera’s shutter state. The apparent speed of the target object in the captured images is maintained at zero to suppress motion blur when the shutter is open, and the camera’s position returns to its home position when the shutter is closed. Our motion-blur-free microscope can shoot non-blurred 512×512 images at 125 fps with frame-by-frame intermittent tracking for objects moving unidirectionally. Compared with the degradation in video that was recorded without tracking, our method reduces image degradation from motion blur 1/40 times or less without decreasing the exposure time when a 10× objective lens is attached. Its performance is verified by showing the experimental results from several moving scenes in microscopic view.