In order to explore the molecular mechanism of the formations of Cymbidium hybrid flower color and scent, we got transcriptomic data of Cymbidium hybrid ‘Yufeng’ (K18, yellow) and ‘Fuyundanxia’ (K24, purplish red) for different flowering stages by RNASeq technique and analyzed the expression levels of genes related to flower color or scent. Present transcriptomic datas provide an important reference for the directional improvement of flower color or scent and creation of special breeding varieties. The results showed that: (1) a total of 11 914 and 6 793 differentially expressed genes (DEGs) were selected in K18 and K24, respectively; of which 58 DEGs related to flower color and scent formation base on kyoto encyclopedia of genes and genomes (KEGG) annotation. Further analysis indicated that flavonoids are the main flower pigment in K18 and K24 and expression of synthetic genes were upregulated significantly at bud stage. Among them, flavonols were generated by chalcone flavanone isomerase gene (CHI), flavonoid 3′5′hydroxylase gene (F3′5′H) and flavonol synthase gene (FLS) in K18; Anthocyanins were got by anthocyanidin synthase gene (ANS) in K24. (2) qRTPCR analysis showed that the expression levels of hydroxymethylglutarylCoA synthase gene (HMGS), hydroxy3methylglutaryl coenzyme A reductase gene (HMGR2), mevalonate5diphosphatase gene (MVD) and so on in terpenoid skeleton biosynthesis all are the highest at the flowering period in K18. Moreover, the expression levels of six TPSs in K18 were more than 100 times than that in K24. (3) Quantitative analysis showed anthocyanin content in K18 (122.28 μg·g^-1) was about 20% of that in K24 (608.74 μg·g^-1). The main pigment component in K24 was cyanidin, which made the flower color red, while the delphinin level in K18 was relatively high (the yellow flower). Study speculated that the overexpression of ANS may be one of the reasons for higher anthocyanin content in K24 petals than that in K18. Flavonol rather than anthocyanin was accumulated in K18 through CHI, F3′5′H and FLS pathway, which affects the determination of flower color.