3D-printed porous bionic scaffolds are dedicated to imitating irregular bone shapes and providing a suitable growth environment for integrated bone tissue. Although many bionic structures have emerged, it needs to be determined which structure has the best osseointegration ability. This study found that the trabecular bone structure was ellipsoid-like by scanning human bone specimens. It is speculated that the bionic scaffold produced using the ellipsoid intersection model has better osseointegration properties. In this study, the computer-aided design (CAD) was used to contrive porous scaffolds with pores of three different geometric shapes, including tetrahedron (TBC), Schwarz-P (P) and ellipsoid bionic structure (EB), and the scaffolds were prepared by selective laser melting (SLM) 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 the rabbits. The micro-computed tomography (Micro-CT) quantitative analysis and hard tissue section staining performed on the samples harvested six weeks and 12 weeks after surgery showed the absolute advantage of EB structure in bone ingrowth, consistent with the results of the in vitro cell experiments. According to computer fluid dynamics (CFD) simulations, the EB structure has the most appropriate internal streamline structure and the best wall shear stress (WSS) distribution for cell proliferation, demonstrating its benefits in osseointegration. The pore geometry has a significant effect on the osseointegration of the scaffold. The ellipsoid bionic structure proposed for the first time in this study is much superior to the regular tetrahedral structure and Schwarz-P curved surface structure in osseointegration, which provides a reference for further future research on appropriate 3D-printed bionic porous scaffolds.