We present a blink-spot projection method for observing moving three-dimensional (3D) scenes. The proposed method can reduce the synchronization errors of the sequential structured light illumination, which are caused by multiple light patterns projected with different timings when fast-moving objects are observed. In our method, a series of spot array patterns, whose spot sizes change at different timings corresponding to their identification (ID) number, is projected onto scenes to be measured by a high-speed projector. Based on simultaneous and robust frame-to-frame tracking of the projected spots using their ID numbers, the 3D shape of the measuring scene can be obtained without misalignments, even when there are fast movements in the camera view. We implemented our method with a high-frame-rate projector-camera system that can process 512×512 pixel images in real-time at 500 fps to track and recognize 16×16 spots in the images. Its effectiveness was demonstrated through several 3D shape measurements when the 3D module was mounted on a fast-moving six-degrees-of-freedom manipulator.