Transition metal catalyzed C–H bond direct activation has gradually developed as one of the most effective tools in synthetic chemistry and is an essential part of drug research and development, which can provide functionalized bioactive molecules in an efficient and selective fashion. The research progress of transition metal-catalyzed C–H bond late-stage functionalization of bioactive molecules in the past decade is summarized from three aspects: C–C, C–O and C–N bond formation. The limitations and future development are reviewed and prospected.