Tissue engineering has emerged as a promising approach for the repair and functional reconstruction of damaged tissues. The bionic and intelligentized scaffolds provide the structural support for cell growth and differentiation as well as tissue regeneration. The surface properties of the biological material implant, the nanotopology in particular, become key aspects in determining the success of the implant. Mesenchymal stem cells (MSC) are widely favored by researchers as the seed cells in tissue engineering. Recently, it has been shown that nanotopographical characteristics of biomaterials regulate a wide range of MSC properties from their cellular behavior and differentiation potential. Herein, this review will provide an update on studies investigating the roles of nanotopography in the development of tissue engineering using MSC.