Direct Manipulation Video Navigation (DMVN) systems allow a user to navigate a video by dragging an object along its motion trajectory. These systems have been shown effective for space-centric video browsing. Their performance, however, is often limited by temporal ambiguities in a video with complex motion, such as recurring motion, self-intersecting motion, and pauses. The ambiguities come from reducing the 3D spatial-temporal motion (x, y, t) to the 2D spatial motion (x, y) in visualizing the motion and dragging the object. In this paper, we present a 3D DMVN system that maps the spatial-temporal motion (x, y, t) to 3D space (x, y, z) by mapping time t to depth z, visualizes the motion and video frame in 3D, and allows to navigate the video by spatial-temporally manipulating the object in 3D.We show that since our 3D DMVN system preserves all the motion information, it resolves the temporal ambiguities and supports intuitive video navigation on challenging videos with complex motion.