ABSTRACT: Background Myricaria laxiflora, an endangered species endemic to the water-level fluctuation zone of the Yangtze River, plays a critical role in riparian ecosystem conservation. However, a comprehensive understanding of its organ-specific metabolic composition remains scarce. Method A non-targeted metabolomic approach incorporating Pearson correlation analysis, principal component analysis, differential metabolite screening, and KEGG pathway enrichment analysis, was utilized to investigate the tissue-specific metabolic profiles across M. laxiflora organs (root, stem, leaf, and flower. Results A total of 1377 metabolites were identified, with secondary metabolites comprising the largest proportion, predominantly terpenoids and flavonoids. Differential metabolite analysis revealed the highest number of dominant metabolites in root (R, 289), followed the flower (F, 97), stem (S, 66), and leaf (L, 26). Terpenoids were most abundant in F and R, while flavonoids were more prevalent in S and L. KEGG pathway enrichment analysis revealed all four organs shared key flavonoid-related pathways, with organ-specific enrichments observed. F uniquely displayed a terpenoid-focused metabolic profile, L exhibited the most diverse set of pathways, including monoterpenoid biosynthesis, S showed substantial overlap with L, and R was the only organ enriched in all three flavonoid-related pathways. Reconstruction of the flavonoid biosynthesis pathway revealed distinct metabolic flux partitioning: F directed flux toward apigenin and kaempferol branches, L accumulated naringenin and quercetin, S contained a broad array of flavonoids, and R acted as a hub for upstream intermediates. Conclusion These results highlight significant organ-specific metabolic specialization in M. laxiflora, with a coordinated spatial distribution of secondary metabolic pathways. This metabolomic profile provides a robust foundation for understanding the species’ metabolic adaptations and highlights its potential as a source of bioactive terpenoids and flavonoids for further pharmacological investigation.
