Considerable studies have focused on the neural basis of visually guided tracking movement in the frontoparallel plane, whereas the neural process in real-world circumstances regarding the influence of binocular disparity and motion-in-depth (MID) perception is less understood. Although the role of stereoscopic versus monoscopic MID information has been extensively described for visual processing, its influence on top-down regulation for motor execution has not received much attention. Here, we orthogonally varied the visual representation (stereoscopic versus monoscopic) and motion direction (depth motion versus bias depth motion versus frontoparallel motion) during visually guided tracking movements, with simultaneous functional near-infrared spectroscopy recordings. Results show that the stereoscopic representation of MID could lead to more accurate movements, which was supported by specific neural activity pattern. More importantly, we extend prior evidence about the role of frontoparietal network in brain-behavior relationship, showing that occipital area, more specifically, visual area V2/V3 was also robustly involved in the association. Furthermore, by using the stereoscopic representation of MID, it is plausible to detect robust brain-behavior relationship even with small sample size at low executive task demand. Taken together, these findings highlight the importance of the stereoscopic representation of MID for investigating neural correlates of visually guided feedback control.