Phosphorus is widely present in living organisms and nature and exists in a variety of isomers with variable crystal structures. There are several common phosphorus monomers in biomedicine, including red phosphorus (RP), black phosphorus (BLK-P), violet phosphorus (VP), and blue phosphorus (BLU-P). Phosphorus-based semiconductor materials (PSCM) have adjustable band gaps, high photogenerated carrier mobility, and efficient photothermal conversion as well as good biocompatibility and degradability. In addition, phosphorus, an essential element for life-sustaining activities, is present in all cells of the human body, accounting for approximately 1% of the body's total weight. Therefore, phosphorus-based nanomaterials have extensive applications in the biomedical field. This review will clarify the classification, preparation methods, physicochemical properties, mechanisms of action, and applications in biomedicine of phosphorus-based nanomaterials while also offering new ideas for their development in biomedicine.