3D-printed porous bionic scaffolds are used to imitate irregular bone shapes and provide a suitable growth environment for integrated bone tissue. Although many bionic structures have emerged, it remains to be determined which structure has the best osseointegration ability. In this study, we found that the trabecular bone structure is ellipsoid-like by scanning human bone specimens. It is speculated that the bionic scaffold produced using the ellipsoid intersection model has better osseointegration properties. Subsequently, computer-aided design was used to contrive porous scaffolds with pores of three different geometric shapes, including tetrahedron (TBC), Schwarz-P (P), and ellipsoid bionic (EB) structures. The scaffolds were prepared by selective laser melting with similar porosities (65%) and pore sizes (480 μm). Mechanical tests have proven the scaffolds to have high accuracy and good mechanical properties. Subsequently, three scaffolds were implanted into the lateral condyle femur of rabbits. Micro-computed tomography quantitative analysis and hard tissue section staining were performed on samples harvested 6 and 12 weeks after surgery. The results demonstrated the advantage of EB structure in bone ingrowth, consistent with the results of the in vitro cell experiments. According to computer fluid dynamics simulations, the EB structure has the most appropriate internal streamline structure and the best wall shear stress distribution for cell proliferation, demonstrating its benefits in osseointegration. The pore geometry has a significant effect on the osseointegration of the scaffold. The EB structure, proposed for the first time in this study, demonstrates significantly superior osseointegration compared to the regular TBC structure and P-curved surface structure, thereby providing a reference for future research on optimal 3D-printed bionic porous scaffolds.