The auxetic structures are highly effective in bone implants due to their unique deformation characteristics. However, ideal tissue engineering scaffolds must possess suitable mechanical properties and biocompatibility. The biological effects of auxetic structures require further study. In this study, three types of 3D re-entrant honeycomb structures with varying angles of 75°, 90°, and 105° were designed. These structures were fabricated by stereolithography 3D printing technology. Finite element simulations and compression tests were conducted to evaluate their mechanical properties. Scaffolds were inoculated with preosteoblast MC3T3-E1 cells, and cyclic loading was applied to investigate the influence of structural and mechanical stimulation on cell arrangement and proliferation. The results demonstrated that the 75° scaffold exhibited auxetic characteristics in all compression directions and possessed anti-fracture properties. The 75° scaffold also promoted cell proliferation by structural design. Cyclic compression facilitated the nuclear translocation of YAP, further enhancing cell growth. The combination of anti-fracture properties and the promotion of cell proliferation makes auxetic structures highly promising for extensive applications.