Mechanical microenvironments, such as characteristics defining mechanical environments and fluid flow play an important role in steering the fate of mesenchymal stem cells (MSCs). However, the synergistic effect of adhesion morphology and fluid flow on the biological behavior of MSCs is seldom investigated. In this article, 0.5 or 0.8 Pa fluid shear stress (FSS) was applied to the MSCs on micropatterned substrates, and the apoptosis and osteogenic differentiation of MSCs were measured by double fluorescent staining. Results showed that the cellular adhesion patterns with low circularity and large area are beneficial to the osteogenic differentiation of individual MSCs. Meanwhile, FSS facilitated osteogenic differentiation of MSCs, as shown by the expression of alkaline phosphatase, osteocalcin, and collagen I. In addition, nuclear transfer of Yes‐associated protein, a transcriptional regulator in MSCs, was enhanced after being exposed to FSS. These results demonstrated the synergistic effects of FSS and adhesion morphology in directing the fate of MSCs, and these effects may be adopted to design bio‐functional substrates for cell transplantation in tissue engineering.