Controlling protein adsorption on material surfaces can offer significant opportunities in terms of engineering the material–cell interactions. In this work, SrTiO3 cubic nanocrystals exposed with {100} facets, which was proved to have strong protein affinity previously, were used to assemble nano-microstructured surface. We demonstrated that the nano-microstructured surface with highly stacking density of the nanocrystals had enhanced cellular responses in cellular adhesion and proliferation compared to that of the (100)-terminated SrTiO3 single crystal substrate. The enhancement is attributed to more interaction sites resulting from heavy protein adsorption on {100} facets of the SrTiO3 cubic nanocrystals, and more appropriate cell growth microenvironment arising from the nanocrystals stacked nano-microstructure. The two factors are suggested to play critical role in material–cell interactions. The SrTiO3 cubic nanocrystals are powerful units to assemble surface nano/microstructure with highly biological responses.