Plant-derived natural products have historically constituted a foundational resource for pharmaceutical development, and the emergence of metabolomics as a systems-level analytical discipline has substantially augmented the capacity to explore plant chemical diversity in the context of drug discovery. Metabolomics enables the comprehensive, simultaneous analysis of low-molecular-weight metabolites present in biological systems, thereby providing an integrated biochemical portrait of plant organisms under defined physiological or experimental conditions. The objective of this review is to critically examine the role of plant metabolomics in modern drug discovery, with emphasis on the analytical methodologies that underpin metabolite identification and quantification, the integration of metabolomic data with complementary omics platforms, and the translational potential of metabolomic findings from bench to clinical and industrial application. Advanced analytical techniques including liquid chromatography-mass spectrometry, gas chromatography-mass spectrometry, high-resolution mass spectrometry, and nuclear magnetic resonance spectroscopy are systematically discussed in relation to their capabilities and limitations in the profiling of plant secondary metabolites. The review further addresses bioinformatic challenges associated with large-scale metabolomic datasets, the use of metabolomics in biomarker discovery and lead compound identification, and the regulatory and reproducibility considerations that govern the translation of plant metabolomic findings into pharmaceutical products. Future perspectives highlight the convergence of artificial intelligence, multi-omics integration, and green chemistry principles as transformative forces in metabolomics-driven drug discovery.