Over the past few decades, tremendous progress has been made in the development of engineering nanomaterials, which opened new horizons in the field of diagnosis and treatment of various diseases. In particular, self-assembled organic nanomaterials with intriguing features including delicate structure tailoring, facile processability, low cost, and excellent biocompatibility have shown outstanding potential in biomedical applications because of the enhanced permeability and retention (EPR) effect and multifunctional properties. In this review, we briefly introduce distinctive merits of self-assembled organic nanomaterials for biomedical applications. The main focus will be placed on summarizing recent advances in self-assembled organic nanomedicine for drug delivery, bioimaging, and cancer phototherapy, followed by highlighting a critical perspective on further development of self-assembled organic nanomaterials for future clinical translation. We believe that the above themes will appeal to researchers from different fields, including material, chemical, and biological sciences, as well as pharmaceutics.