Objective To simulate the flow field within large scale porous β-TCP scaffold in perfusion bioreactor. Method The computational fluid dynamics (CFD) method was used to simulate the flow conditions within large scale porous β-TCP scaffold in our newly designed perfusion bioreactor. The velocity field and the flow shear stresses within the scaffold at different perfusion flow rates were estimated by our simulation model. Result The velocity field and the flow shear stress throughout the scaffold could be well simulated with this method. The corresponding flow velocities in the scaffold pores at flow rate of 3 ml/min, 6 ml/min and 9 ml/min were (0227±0.062) mm/s, (0.459±0.125) mm/s and (0.701±0.193) mm/s. The flow shear stresses within the scaffold at flow rate of 3 ml/min, 6 ml/m in and 9 ml/min were 52±1.5 mPa, 1.06±3 mPa and 162±4.6 mPa respectively. Conclusions This simulation modeling could be used to compare results obtained from different perfusion bioreactor systems or different scaffold microarchitectures. It could allow specific shear stresses to be determined that optimize the distribution, proliferation or differentiation of seeded cells and the microarchitectures of the scaffold.