Controlling cell organization is still a major bottleneck in biointerface engineering when the material dimensions decrease to the nanoscale. Here, Au nanowire-patterned array platforms with multiscale design from the macroscale to the nanoscale are developed for studying human bone marrow-derived mesenchymal stem cell (hBM-MSC) response. When the angle of the Au nanowires on glass is increased from 0 degrees to 90 degrees, hBM-MSC arrangement exhibits a transition from a unidirectional distribution induced by a vector response to a bimodal polarization pattern. The degree of cell vector response and elongation decreases with increasing nanowire angles from 0 degrees to 90 degrees. Further, it is demonstrated that the specific cell adhesion and organization are dependent on the surface micro/nanotopography, which is greatly enhanced by introducing stem cell-material affinity differences. An ideal model and new insights into a deeper understanding of cell-nano-biointerface interactions are provided.