Multifunctional nanoparticles (NPs) have been widely used in biomedical applications because of their versatile properties. The properties of NPs should be well designed and controlled according to various applications because they may directly affect the functions and performances of NPs in biological systems. Cellular uptake is a prerequisite for the success of NP-based biomedical applications. However, the internalized NPs inside cells may have some adverse effects. Therefore, the interactions between NPs and cells should be thoroughly investigated and elucidated. This review summarizes the latest advances in NP-cell interactions. Especially the effects of NP properties including size, shape, shell structure, surface chemistry and protein corona formation on cellular uptake and cytotoxicity are highlighted in detail. Their effects on cell proliferation, differentiation and cellular mechanics are also discussed. These insights into NP-cell interactions should provide useful information for the preparation of highly functional NPs and their biomedical applications.