Mini-implant anchorage for the orthodontic treatment is an effective method to reinforce anchorage. The stability is critical in the achievement of reliable anchorage. Three-dimensional finite element analysis is one of the most effective method to analyze biomechanics and simulate stomatognathic system, which has been widely used in orthodontic research. We summarized the current literature on the use of the three-dimensional finite element method in primary stability of mini-implant anchorage from aspects of mini-screw implants, bone and operation, in order to improve success of implant.