The construction of porous scaffold structures using finite element model allows a bone scaffold to mimic the bio mechanical characteristics of natural bone. The flexibility in designing a three-dimensional (3D) scaffold solved the difficulties such as the stress shielding effect and prevent implant failure. However, fabricating the scaffold functioning as an extracellular matrix and liable for cell proliferation with excellent material and design parameters to match the natural bone property is still challenging. This study aimed to analyze the porosity and mechanical properties of beta-tricalcium phosphate and hydroxyapatite (HA) scaffolds with honeycomb, circular, and elliptical unit cell types with pore sizes ranging from 250 to 550 µm. SOLIDWORKS software was used to build a 3D design for bone scaffold models. Finite element analysis using ANSYS software was used to model and analyze scaffold samples. According to computational analysis, mechanical characteristics of models showed that when porosity increases, the value of young’s modulus and compressive strength falls. The 3D honeycomb bone scaffold with HA material attributes similar to natural bone properties. The permeability values for honeycomb, circular and ellipse structures of the scaffold architecture varied from 3.77 × 10−9 m2 to 1.04 × 10−7 m2, 4.89 × 10−9 m2 to 1.50 × 10−7 m2 and 5.7 × 10−9 m2 to 1.76 × 10−7 m2, respectively. The distribution of wall shear stress of the scaffolds reduces as the porosity rises, in contrast to the permeability values. Therefore, the findings of this study may pave the way to enhance bone scaffold development in tissue engineering.