Objective To evaluate the influence of stress distribution on bone-anchored maxillary protraction with different protraction sites using biomechanical method, to direct the clinical. Method To build a three-dimensional finite element model of children’s head which includes implant anchorages. Four position of implants (distal of primary lateral incisor, mesial of maxillary first primary molar, mesial of maxillary first molar, distal of maxillary first molar) were loaded separately. The finite element models were loaded as 500g each side and 30° forward direction to the occlusal plane. Stress distribution of each sutures were analysed. Results The maximum stress value of Frontomaxillary Suture was in condition II (2.819×10-2-1.477×10-3MPa). The maximum stress value of Nasomaxillary Suture was in condition I (9.24×10-4-5.296×10-6MPa). The maximum stress value of Zygomaticomaxillary Suture was in condition IV (1.313×10-2-3.947×10-4MPa). The maximum stress value of Zygomaticofrontalis Suture was in condition IV (3.169×10-2-4.952×10-4MPa). The maximum stress value of Zygomaticotemporal Suture was in condition III (1.587×10-2-1.148×10-3MPa). The maximum stress value of Medianpalatine Suture was in condition I (7.300×10-4-6.479×10-6MPa). Conclusions It could improve class III profile especially in the nose root when the protraction sites were put in the distal maxillary primary lateral incisor and the mesial maxillary first primary molar. It is of positive significance to improve class III profile especially in the maxillary basal bone of the midface when the protraction sites were put in the mesial or distal maxillary first molar.