Objective To observe the effect of mini-implant lengths on stress distribution in peri-implant surface. Methods The 3D finite element analysis mandible and mini-implant models with diameter of 1.6 mm, lengths of 6, 8, 10 and 12 mm were established. The mini-implants were inserted into designed site of mandibular vertically, respectivly. A force of 1.96 N were applied mesioly and 45° tilted mesio-vertically in models. The stress distribution under every condition was recorded and analyzed. Results When load was applied mesially, the maximum stress varied from 3.500 to 3.765 MPa, the maximum displacement varied from 1.266 to 1.288 μm. When load was applied 45° tilted mesio-vertically, the maximum stress varied from 4.075 to 4.510 MPa, the maximum displacement varied from 1.668 to 1.694 μm. All of the maximum stress and displacement of loading mesially were lower than loading mesiovertically. Conclusion The change of the mini-implant length within 6-12 mm don’t show much influence on the stress distribution. The loading type is an important factor influencing stress and displacement of peri-implant bone.