Porous scaffolds, whose mechanical and biological properties are greatly affected by structure, are new treatments for bone defects. Since bone repair is related to biomechanics, analyzing the osteogenesis in scaffolds based on mechanical stimulation may become a more effective method than traditional biological experiments. A tissue regeneration algorithm based on mechanical regulation theory was implemented in this study to evaluate the osteogenesis of classical scaffolds (Gyroid, I-WP, and Diamond). In vivo experiments were used to verify and supplement the simulation results. Different approaches to describing osteogenesis were discussed. Bone formation was more obvious inside the Gyroid scaffold and outside the I-WP scaffold, while the new bone was more sufficient and evenly distributed in the Diamond scaffold. The osteogenesis pattern of the bone scaffold in the simulation analysis was consistent with the results of animal experiments, and the bone volume calculated by the tissue fraction threshold method and the elastic modulus threshold method was very similar to the in vivo experiment. The mechanical responses mediated by structure affect the osteogenesis of bone scaffolds. This study provided and confirmed a simulation analysis method based on mechanical regulation theory, which is more efficient and economical for analyzing tissue healing in bioengineering.