In order to explore the molecular mechanism of the formation of Cymbidium ensifolium flowercolor, we used highthroughput highseq sequencing technique to construct transcriptome library with the yellowgreen and red petals of one Cymbidium plant as experimental materials in this study. We investigated about the biosynthesis metabolism pathway of color related ingredients, the transcriptional activity of key regulatory genes, etc. The results showed that: (1) a total of 131 110 030 Clean Reads and 106 479 Unigenes were obtained by transcriptome sequencing, and 29 748 Unigenes with annotated information was obtained by comparing with NR, GO, COG, KEGG and other public databases; (2) in contrast to yellowgreen petals, the expression of 776 genes increased and 589 genes decreased in red petals, were identified to 93 metabolic pathways by KEGG database, and of which 6 pathways and total 20 differentially expressed genes (83 Unigenes) are related to flavonoid biosynthesis; (3) qRTPCR analysis showed that the expression ratio trend of the selected 20 genes in Cymbidium petals is consistent with the transcriptome ratio trend of FPKM, which means the transcriptome data obtained in this study has a high reference value. Among them, the upregulation genes of chorismate mutase (CM), phenylalanine ammonialyase (PAL) and cinnamate 4hydroxylase (C4H), 4coumarate: CoA ligase (4CL) are in favor of flavonoid precursor accumulation. Chalcone synthase (CHS), dihydroflavonol4reductase (DFR) and anthocyanidin synthase (ANS) were almost no expressed in yellowgreen petals, but significantly increased in the red petals, which are possibly connected with the floral color formation of Cymbidium ensifolium.