The unique properties of nanomaterials in drug delivery and tissue engineering have captured a great deal of attention as experimental tools in bioimaging, diagnostic, and therapeutic processes. A plenty of research have provided a strong evidence that nanostructures not only passively interact with cells but also actively engage and mediate cell functions and molecular processes. Undoubtedly, it is crucially important to better understand biological responses to engineered nanomaterials, especially in view of their potential for biomedical applications. In this review, we shall highlight recent advances in exploring nano-bio effects in diverse systems of nanoparticles, nanotopographies, and mixed composite scaffolds. We will also discuss their manipulating functions on cellular behaviors and important biological processes of adhesion, morphology, proliferation, migration, differentiation, and even hidden mechanisms including molecular signaling pathways. At last, the perspectives will be addressed for further directions of nanomaterial designs with the purpose of better drug delivery and cell therapies.