The invention belongs to the technical field of oral scanning, and discloses a direct three-dimensional scanning method and system for a physiological motion boundary of oral soft tissue. The direct three-dimensional scanning system for the physiological motion boundary of the oral soft tissue comprises an oral image acquisition module, an oral image processing module, an oral image segmentation module, a central control module, a non-motion area acquisition module, a direct three-dimensional scanning module, a three-dimensional scanning data acquisition module, a data storage module, a terminal module and a display module. The scanning system provided by the invention is high in scanning speed, high in precision and simple to operate; an active contour method is used for semi-automatically carrying out labeling segmentation on an oral medical image serving as a training set, and the semi-automatic method improves the accuracy and timeliness of labeling segmentation; and a confrontation generation network is used for automatically generating a segmentation result of the oral medical image, so that the complete and effective expression of the healthy oral physiological structure isbalanced in key indexes such as segmentation precision, efficiency, stability and robustness.