Abstract: To explore the key metabolites and pathways related to the formation of fragrance in the native species of Phalaenopsis and to screen for superior fragrant parents and identify target genes for molecular breeding, thereby restoring and improving the fragrant traits of cultivated Phalaenopsis. In this study, GC-MS wide-targeted metabolomic analysis was conducted on the floral tissues of nine native Phalaenopsis species at full bloom. A total of 214 secondary metabolites were identified, mainly including organic acids and their derivatives (56.3%), benzene and its substituted derivatives (21.5%), and lipids (12.0%). PCA and cluster analysis showed significant metabolic profile differentiation among species (cumulative contribution rate of 44.2%). Among them, phenylacetaldehyde was highly accumulated in Phalaenopsis philippinensis (4.18%), while it was undetectable or present at extremely low levels in the other species. Considering its extremely low odor threshold (～0.02 ppb), it is suggested to be a key fragrant component. KEGG enrichment analysis indicated that phenylalanine metabolism, carbon metabolism, and phenylpropanoid biosynthesis pathways were significantly enriched. Although this study was based on tissue extraction and reflected the potential fragrance precursor pool, it still clarified the core metabolic modules driving fragrance diversity. Phalaenopsis philippinensis can be used as an excellent fragrant parent, and key enzyme genes in the phenylalanine pathway can be used as targets for molecular breeding or metabolic engineering to improve the fragrance quality of cultivated Phalaenopsis in a targeted manner.