Metal-organic frameworks (MOFs) have aroused great interest in the field of nanoscience and nanotechnology particularly in biomedical domains, such as drug delivery system (DDS), biomedical imaging (BI) and photodynamic therapy (PDT). As an emerging material, MOFs exhibit extraordinarily high specific surface area, controllable particle size and good biocompatibility. With extraordinary flexibility of selection of organic and inorganic components, MOFs can be rationally tuned with versatile structures and porosities. MOFs can serve as ideal vehicles for DDS, BI and PDT through modification and function. In this review, we had summarized the design and synthetic strategies for preparing MOFs as well as introduced their recent advances in DDS, BI and PDT. Finally, the prospect and future challenges of the nanomaterials are prospected.