Based on fast marching watersheds and marker-controlled method, a teeth model segmentation algorithm for Virtual Orthodontics System is presented in this paper. Three critical techniques: interactive marker, threshold setting and stack operation theory, is used in the algorithm. To reduce stack operations, a combination technique of automatic threshold setting and manual threshold regulating is proposed, which obviously overcome the difficulty in intuitional segmentation control, solve the maneuverability of threshold, improve the segmentation quality and reduce the running time of segmentation process. The output results show that the segmentation algorithm in the paper has high efficiency and excellent segmentation outcome.