Objective: The purpose of this study was to investigate the stress distribution on the orthodontic mini-implant (OMI) surface and periodontal ligament of the maxillary first and second molars as well as the tooth displacement according to the OMI position in the dragon helix appliance during scissors-bite correction. Methods: OMIs were placed at two maxillary positions, between the first and the second premolars (group 1) and between the second premolar and the first molar (group 2). The stress distribution area (SDA) was analyzed by three-dimensional finite element analysis. Results: The maximal SDA of the OMI did not differ between the groups. It was located at the cervical area and palatal root apex of the maxillary first molar in groups 1 and 2, respectively, indicating less tipping in group 2. The minimal SDA was located at the root and furcation area of the maxillary second molar in groups 1 and 2, respectively, indicating greater palatal crown displacement in group 2. Conclusions: Placement of the OMI between the maxillary second premolar and the maxillary first molar to serve as an indirect anchor in the dragon helix appliance minimizes anchorage loss while maximizing the effect on scissors-bite correction.