In order to confirm the molecular basis underlying flower color variegation between Cymbidium hybrid ‘Yufeng’ and its mutant ‘Shuangyijinlong’, we used targeted metabolomics and transcriptomics to identify the differentially expressed metabolites (DEMs) and differentially expressed genes (DEGs) involved in flavonoid biosynthesis. The results showed that: (1) by using targeted metabolomics techniques, we identied 271 flavonoid metabolites, in which 30%-50% metabolites were flavonols and flavonoid metabolites. A total of 38 DEMs (15 up-regulated, 23 down-regulated) were identified. Among these, the content of dihydrokaempferol-7-O-glucoside (flavonol) in ‘Yufeng’ was 124 444 times of which was in ‘Shuangyijinlong’, while the content of uralenol (flavonol) in ‘Shuangyijinlong’ was 7 244 times of which was in ‘Yufeng’. (2) KEGG analysis showed that flavonoid biosynthesis, flavone and flavonol biosynthesis were significantly enriched. In flavonoid biosynthesis pathway, the contents of phlorizin, xanthohumol, dihydrokaempferol, dihydromyricetin and epigallocatechin all increased, the contents of naringin and dihydroquercetin decreased. In addition, the contents of trifolin and quercetin decreased in flavone and flavonol biosynthesis pathway. (3) By the transcriptome, a total of 563 DEGs were identified, 220 (39.1%) DEGs of which were up-regulated and 343 (60.9%) DEGs were down-regulated in the ‘Yufeng’ vs. ‘Shuangyijinlong’ comparison. KEGG analysis indicated that flavonoid biosynthesis-related DEGs (CCoAOMT, CHS, CHI, F3H and FLS) were found to be signiflcantly enriched. (4) QRT-PCR validation showed that the expression level of flavonoid biosynthesis-related DEGs (CHS2, CHS3, CHI, F3H and FLS) and transcription factor gene HD-ZIP were lower in ‘Shuangyijinlong’ than those in ‘Yufeng’. In general, the expression of genes showed a same trend to the accumulation of metabolites, suggesting that the color change of ‘Shuangyijinlong’ might be attributed to the down-regulation of CHS, CHI, F3H and FLS that led to block the downstream metabolites synthesis. It is speculated that the genes involved in the flavonoids biosynthesis may be the key genes for the flower color variegation in Cymbidium hybrid.