An ideally designed scaffold for tissue engineering must be able to provide an environment that recapitulates the physiological conditions to control stem cell function. Here, we compared vertically aligned single-crystal apatite nanowires sheathed in graphitic layers (SANGs) with single-crystal apatite nanowires (SANs), which had the same geometric properties as-but differing nanotopographic surface chemistry than-SANGs, in order to evaluate the effect of the graphitic layer on the behavior of human mesenchymal stem cells (hMSCs). The difference in nanotopographic surface chemistry did not affect hMSC adhesion, growth, or morphology. However, hMSCs were more effectively differentiated into bone cells on SANGs through interaction with graphitic layers, which later degraded and thereby allowed the cells to continue differentiation on the bare apatite nanowires. Thus, SANGs provide an excellent microenvironment for the osteogenic differentiation of hMCS.