Since its conceptual inception in 1995, Molecular Pharmacognosy has evolved over three decades from a nascent idea into a frontier interdisciplinary discipline characterized by a comprehensive theoretical system, mature methodologies, and extensive applications. This paper systematically reviews the significant milestones of this discipline in theoretical innovation, technical standardization, industrial application, and platform construction. It highlights breakthrough achievements in areas such as technical standards for the molecular identification of crude drugs, elucidation of the formation mechanisms of Dao-di herbs, establishment of conservation models for rare and endangered resources, and biosynthesis of active compounds. The paper further elucidates the evolutionary research paradigm of Molecular Pharmacognosy. Originating from phenomena observed in both the discipline and the industry, this paradigm advances through a progressive cycle of problem derivation—hypothesis presupposition—technical innovation—theoretical enrichment, driven by the dynamic interplay between theory and practice. Furthermore, the paper analyzes current challenges regarding the precision of molecular identification, the complex mechanisms of geo-authenticity, and the sustainable utilization of resources. Molecular Pharmacognosy is poised to integrate deeply with frontier technologies such as artificial intelligence, pan-omics, quantum computing, biomanufacturing, smart breeding, and gene editing. This integration will drive a revolutionary shift in the research paradigm from recognition and revelation to prediction and design. Ultimately, these achievements will mark a new phase defined by precision, systematization, and engineering, injecting fresh momentum into the modernization of TCM.