Objective To analyze the mechanical properties of bone tissue engineering scaffolds with different pore structure and porosity, and improve the mechanical properties of scaffolds by changing pore structure. Methods Square pore, spherical pore and cylindrical pore with different porosities from 55% to 75% were established by SolidWorks software, and the surface-volume ratio of different structures was calculated. The stress distribution and equivalent compression modulus of different scaffolds were obtained by ANSYS Workbench software. According to the stress distribution results, the scaffold with rectangular pore structure and cuboid element structure was improved instead of square pores. Results With the increase of porosity, the surface-volume ratio of the three structures increased. For the same porosity, the surface-volume ratio of square pores and spherical pores was larger, while that of cylindrical pores was the smallest. The modulus and porosity of the three structures were approximately linear. The modulus of the square pore and the cylindrical pore were similar. The stress analysis on the square pore and two improved structures with 60% porosity showed that for the two improve structures, the wall stress on 4 edges parallel to the direction of applied stresses could be reduced by 15%. Conclusions The surface-volume ratio and mechanical property of square pores were more advantageous than spherical pores and cylindrical pores with the same porosity, and the two improved structures could improve the mechanical properties of square pores. The two improved pores enriched the structure of tissue engineering scaffolds. The research findings provide the mechanical references for their clinical application.