Background: Because of osteoporosis, traffic accidents, falling from high places and other reasons, the vertebral body could be compressed injury, even collapse. Vertebral implant can be used for clinical treatment. Because of the advantages of honeycomb sandwich structure, such as low cost, less material, light weight, high strength, and good cushioning performance, honeycomb sandwich structure was used as the basic structure of vertebral implant.Methods: In this paper, we applied the orthogonal experiment method to analyze the size effect of honeycomb sandwich structure by finite element method. Based on the minimum requirements of three indexes of peak stress, axial displacement, and anterior-posterior displacement, the optimal structure size was determined. Further, through local optimization of the overall structure of the implant, we designed better honeycomb sandwich structure vertebral implant.Results: The optimal structure size combination is determined as the face sheets thickness 1mm, wall thickness 0.49mm, cell side length 1mm, height 6mm. Than through local optimization, the peak stress is further reduced, the overall stress distribution is uniform, and the deformation is reduced. The optimized peak stress decreases to 1.041MPa, the axial deformation is 0.111%, and the anterior-posterior deformation is 0.014%. The honeycomb sandwich structure vertebral implant with stable structure and good mechanical performance was designed.Conclusions: The research result provides a method for the optimal design of vertebral body implant structures, as well as provides a new idea and biomechanical basis for clinical treatment after vertebral body injury.