Objective To investigate the effect of different perfusion flow rates on proliferation and osteoblastic differentiation of human mesenchymal stem cells (hMSCs) in large scale β-TCP (tricalcium phosphate) scaffold at perfusion bioreactor. Methods hMSCs isolated from iliac bone marrow aspiration were loaded into large scale β-TCP scaffold and cultured in perfusion bioreactor at the perfusion flow rate of 3, 6 or 9 mL/min for 15 days. The culture media were collected for D-glucose consumption assay every 3 days. After perfusion culture for 15 days, the cell-scaffold composites were harvested for assessment of cell viability by MTT colorimetric method, SEM observation and osteogenic gene expression by real-time PCR. Results The proliferation of hMSCs assayed by daily glucose consumption showed that at early stage of culture, cells proliferated faster at flow rate of 9 mL/min than at 3 or 6 mL/min (P<0.001); while at late stage of culture, cells proliferated faster at flow rate of 6 mL/min (P<0.05). The cell viability indicated that the cell-scaffold composites at flow rate of 6 mL/min exhibited the most viable cells (P<0.001). SEM indicated that all the macropores of the scaffold at different flow rates were filled with cellular layers. All cellular layers at flow rate of 3 mL/min were incompact, but that at 9 mL/min were compact; at flow rate of 6 mL/min, the cellular layers were either compact or incompact. Real-time PCR revealed that after perfusion culture for 15 days, the mRNA expression of osteobalstic genes including ALP and OP, were enhanced significantly at flow rate of 6 and 9 mL/min as compared to that at 3 mL/min (P<0.01); however, the 9 mL/min group presented the higher OC expression than 3 and 6 mL/min group (P<0.001). Conclusions At early stage of perfusion culture, the proliferation of hMSCs was promoted at flow rate of 9 mL/min, while at late stage, there was more viable cells in scaffolds at flow rate of 6 mL/min. The osteoblastic differentiation of hMSCs was facilitated with the increase of perfusion flow rate, which was attributed to the increased flow shear stress.