A major challenge in advancing nanoparticle (NP)-based delivery systems stems from the intricate interactions between NPs and biological systems. These interactions are largely determined by the formation of the NP–protein corona (PC), in which proteins spontaneously adsorb to the surface of NPs. The PC endows the NPs with a new biological identity, capable of altering the interactions of NPs with targeting organs and subsequent biological fate. This review discusses the mechanisms behind PC-mediated effects on tissue distribution of NPs, aiming to provide insights into the role of PC and its potential applications in NP-based drug delivery.