Cell-based therapies are emerging as a promising approach for various diseases. Their therapeutic efficacy depends on rational control and regulation of the functions and behaviors of cells during their treatments. Different from conventional regulatory strategy by chemical adjuvants or genetic engineering, which is restricted by limited synergistic regulatory efficiency or uncertain safety problems, a novel approach based on nanoscale artificial materials can be applied to modify living cells to endow them with novel functions and unique properties. Inspired by natural “nano shell” and “nano compass” structures, cell nanomodification can be developed through both external and internal pathways. In this review, some novel cell surface engineering and intracellular nanoconjugation strategies are summarized. Their potential applications are also discussed, including cell protection, cell labeling, targeted delivery and in situ regulation. It is believed that these novel cell-material complexes can have great potentials for biomedical applications.