Metal-organic frameworks (MOFs) are porous materials composed of metal ions or clusters and organic ligands connected through coordination bonds, exhibiting high specific surface areas, tunable pore structures, and excellent chemical stability. These unique features have enabled MOFs to be widely applied in catalysis, gas separation, and environmental purification. In recent years, the potential of MOFs in the biomedicine field has garnered significant attention. MOFs offer efficient drug loading and controlled release capabilities, particularly for targeted therapies in oncology and other diseases. Furthermore, their structural versatility positions them as promising candidates for antitumor and antibacterial treatments. However, challenges related to biocompatibility, in vivo degradation, and potential toxicity need further investigation. This review explores the latest advancements in MOF applications in biomedicine, focusing on drug delivery, targeted therapy, and modification strategies, as well as toxicity assessment and mechanisms. Finally, future research directions are proposed, including the development of intelligent drug delivery systems, multimodal diagnostic platforms, and optimized MOF designs for clinical translation.