Abstract: The clinical efficacy of Chinese medicines (CMs) fundamentally relies on their material basis, with active constituents serving not only as the cornerstone of CM's pharmacological activity, but also as a valuable resource for innovative drug research and development. However, the precise clinical application and internationalization of CMs have long been hindered by limited understanding of the molecular targets, modes of action, and pharmacological mechanisms underlying their functional components. Novel biochemical and biophysical approaches, in combination with recent advancements in mass spectrometry (MS)-based techniques, instrumentation, and data analysis pipelines, have significantly facilitated the identification of molecular targets and elucidation of pharmacological mechanisms of functional components in CMs. This review summarizes recent advances in the target identification of functional components in CMs and the characterization of small molecule-target protein interactions. We discuss the principles and technical aspects of small molecule-labeled and label-free target deconvoluted strategies leveraging biological mass spectrometry, providing a comparative analysis of their application scopes, strengths and limitations. This review article also addressed the recent progress made by the scholars in characterizing the interaction modes between functional components of CMs and target proteins, using biomass spectrometry and other cutting-edge technologies. The relevant research strategies, methodologies, and application cases are expected to provide a series of solutions and research models for the discovery of targets and in-depth elucidation of pharmacological mechanisms of CMs pharmacodynamic substances.