Manipulating an incorporated scaffold to direct cell behaviors play a key role in tissue engineering. In this study, we developed novel nano-topographic oxidized silicon nanosponges capable of being modified with various chemicals of a few nm in thickness to gain further insight into the fundamental biology of cell-environment interactions in vitro. A wet etching technique was applied to fabricate the silicon nanosponges in a high-throughput manner and was followed by vapor deposition of various organo-silane chemicals to enable self-assembly on the surfaces of the silicon nanosponges. When Chinese hamster ovary cells were cultured on these chemically modified nano-topographic structures, they displayed distinct morphogenesis, adherent responses, and biochemical properties in comparison with those of their planar oxidized silicon counterparts. There were predominant nano-actin punches and slender protrusions formed while cells were cultured on the nano-topographic structures, indicating that cell behaviors can be influenced by the physical characteristic derived from nano-topography, in addition to the hydrophobicity of contact surfaces. This study demonstrates potential applications of these nano-topographic biomaterials for controlling cell development in tissue engineering as well as in basic cell biology research.