<p>Molecular docking, a relatively well-established research instrument, is extensively applied in protein research and drug development. Recently, the technique has also exerted a vital role in nanomedicine research, especially in nanotechnology-based drug design and delivery system research. However, so far no one has sorted out the current situation of this interdisciplinary field. In this review, firstly, the basic principles and methods of molecular docking were introduced; then several specific applications were highlighted in the context of nanomedicine re-search, including nanomaterial modification, screening of nanomedicine carriers, screening (validation) of potential ligands (targets) of nanomaterials, and assessment of the toxicity or biosafety of nanomaterials were summarized; finally, the current challenges of molecular docking in nanomedicine re-search were discussed, and an outlook on its development and optimization was also given. This work is expected to make it easier for researchers to comprehend molecular docking and its applications in nanomedicine.</p>