As a promising delivery nanosystem for drug controlled-release, nanocarriers (NCs) have been investigated widely. Although various studies have concentrated on the preparation and characterization of nanoparticles (NPs), clinical applications are rarely reported, due to the unclear distribution, absorption, metabolism, toxicology processes and drug release mechanism. The clinical application of NCs is therefore still a long way off. This review describes the effects of the properties of NCs (including size, shape, surface properties, porosity, elasticity and so on) on pharmacological and toxicological behaviours in vivo and medical applications. Moreover, this study is intended to help the readers understand the behaviours and mechanisms of NCs and positively face the challenges caused by the variety of complicated and limited processes of NCs in vivo. Importantly, this article provides some strategies for the clinical application of NCs and may provide ideas to enhance the therapeutic efficacy of NCs without increasing the toxicology, by introducing tracing technology, which can be more suitable in contributing to the development of safety and efficacy of NCs and the growth of nanotechnology.