How to design appropriate scaffold structure and mechanical environment for vitro culture of bone tissues are the focus of bone tissue engineering research. The mechanical properties of internal flow field within the scaffold are the most important factors in the scaffold design and cultivation. In order to identify the relationship between perfusion parameters, pore structure and the internal shear stress distribution, a computational scaffold model is proposed, which uses ellipsoid as the basic pore-making unit and uses major axis as the shape control parameter. Computational fluid dynamics simulation shows that the average shear stress on pore walls is linear with the major axis when the bone scaffold porosity is maintained in the same level, and the distribution of shear stress trends to be more uniform with the increase of the major axis. The experiments provide clear relationship between the structure parameter and the distribution of shear stress. And this can be used to improve the pore structure design.