Phosphorus plays an indispensable role in energy metabolism, acid-base balance, and genetic substances transfer. As nanotechnology advances, plenty of phosphorus-based nanomaterials have been developed and widely used in the fields of biology and medicine. The size and structure of phosphorus-based nanomaterials give them unique physicochemical, optical, and biological properties, greatly increasing the variety of nanomedicine. The excellent properties further promote the applications of phosphorus-based nanomaterials in drug nanocarriers, tumor theranostics, biosensors, and bone formation. In this review, we first introduce the phosphorus science to unify current phosphorus-based nanomaterials and discuss their synthesis methods. Furthermore, the representative nanoplatforms utilizing the corresponding properties are highlighted. Finally, research development, potential challenges, and perspectives for further improvement of phosphorus-based nanomaterials in biomedicines are presented.