Objective To study mechanical properties of the bone scaffold with different structure and its internal flow field distributions, so as to provide a direct comparison and judgment on model structure and offer an effective guidance for bone scaffold structure design. Methods Bone scaffold with natural, woven and spherical pore structure were reconstructed respectively by using Pro/Engineer and Mimics. The effective elastic modulus for three kinds of scaffolds, as well as their stress distributions and internal flow field distributions under threedimensional perfusion culture system were analyzed with the finite element method. Results The bone scaffold with natural structure showed smaller effective elastic modulus, smaller peak stress and more uniform stress distributions under the same pressure. With the same initial velocity and fluid viscosity, the bone scaffold with natural structure showed smaller internal velocity, wall shear stress and wall pressure. Conclusions The bone scaffold with natural structure has better biomechanical properties, which corresponds to the design criteria of bone scaffold in bone tissue engineering.