Metabolomics,　a　critical　tool　for　analyzing　small-molecule　metabolites,　integrates　with　genomics,　transcriptomics,　and　proteomics　to　provide　a　systems-level　understanding　of　fungal　biology.　By　mapping　metabolic　networks,　it　elucidates　regulatory　mechanisms　driving　physiological　and　ecological　adaptations.　In　fungal　pathogenesis,　metabolomics　reveals　host-pathogen　dynamics,　identifying　virulence　factors　like　gliotoxin　in　Aspergillus　fumigatus　and　metabolic　shifts,　such　as　glyoxylate　cycle　upregulation　in　Candida　albicans.　Ecologically,　it　highlights　fungal　responses　to　abiotic　stressors,　including　osmolyte　production　like　trehalose,　enhancing　survival　in　extreme　environments.　These　insights　highlight　metabolomics＇　role　in　decoding　fungal　persistence　and　niche　colonization.　In　drug　discovery,　it　aids　target　identification　by　profiling　biosynthetic　pathways,　supporting　novel　antifungal　and　nanostructured　therapy　development.　Combined　with　multi-omics,　metabolomics　advances　insights　into　fungal　pathogenesis,　ecological　interactions,　and　therapeutic　innovation,　offering　translational　potential　for　addressing　antifungal　resistance　and　improving　treatment　outcomes　for　fungal　infections.　Its　progress　shed　light　on　complex　fungal　molecular　profiles,　advancing　discovery　and　innovation　in　fungal　biology.　　©　2025　The　Author(s).