Analysis of the trajectory provides insights into dynamic and complex brain activity responsible for spontaneous behaviors, as eye tracking has contributed to the investigation of the process underlying gaze control during scene perception. In this study, we developed a novel 3D video analysis system that could track the nose of a rat and applied it to analyze spatiotemporal patterns of object exploration. By means of this system, we analyzed object exploration of intact rats during a novel object recognition test, and compared the results in the intact rats with those in rats systematically injected MK-801. The 3D trajectory analysis revealed a specific pattern of object exploration in the sample phase of the novel object recognition test: intact rats first explored the lower parts of objects and then gradually explored the upper parts. The systematic injection of MK-801 suppressed changes in these exploration patterns. Comparison of these data with those analyzed by visual inspection of experts demonstrated that the system could precisely track the nose and detect the nose contact with an object. It is noted that the 3D system can reproducibly and accurately score the novel object recognition test, which represents an advance over previous scoring methods (visual observation and computerized 2D video analysis) in which reproducibility and accuracy are incompatible. The results, along with those of previous studies, suggest that the changes in the exploration patterns reflect neophobia to a novel object and/or changes from spatial learning to object learning. These results suggest that the 3D system has the potential to facilitate future investigation of neural mechanisms underlying object exploration that result from dynamic and complex brain activity.