Three-dimensional multiple object tracking (3D-MOT) has been used in various fields to mimic real-life tracking, especially in perceptual-cognitive skills training for soccer. Yet, the learning efficiency in 3D-MOT tasks has not been compared with 2D-MOT. Further, whether the advantage can be reflected by heart rate variability (HRV) based on the neurovisceral integration model should also be examined. Therefore, we used both 2D- and 3D-MOT in a brief adaptive task procedure for adolescent female soccer players with HRV measurement. A faster tracking speed threshold of participants was found in the 3D- compared to 2D-MOT, as well as average tracking speed in the last training period of 3D-MOT. Moreover, lower low frequency (LF) components of HRV in the 3D-MOT indicated a flow experience, demonstrating the provision of more attentional resources. Therefore, we observed that adolescent female soccer players demonstrated higher learning efficiency in 3D-MOT tasks in virtual reality (VR) through a higher flow experience. This study examined the learning efficiency between the two MOT tasks in the soccer domain using evidence from HRV and highlighted the utility and applicability of 3D-MOT application.