• The yellow color of Mint was mainly affected by the conversion of dihydroquercetin to quercetin by the effect of FLS, and the PH, iron ions and CCD1 could also affect its flower color. • The red color of Mpun was mainly presented by the glycosylation of cyanidin and cyanidin, and copper ions, ZDS, and CCD1 could also affect its flower color. • The blue flower color of Mwil was resulted by the glycosylation of cyanidin, iron ion, oxidation, phosphate ion and other factors. Meconopsis ( Meconopsis spp.) belongs to the family Papaveraceae and is the representative alpine flora in the Pan Himalaya region. Diversity in color is a key taxonomic feature of Meconopsis species, which makes it to be an ideal material for mechanism analysis of petals coloration; however, few studies have focused on this topic. In this study, we selected three Meconopsis species with different flower colors, including M. punicea with red flowers, Meconpsis integrifolia with yellow-green mix flowers, and M. wilsonnii with blue-violet mix flowers. To reveal the coloration mechanisms in Meconopsis , petal samples were collected from each species at three developmental time points (initial, middle, and mature) for RNA sequencing and identification of anthocyanins and flavonoids. Our results showed that the mechanisms of petal coloration were different in selected species, and cyanidin and flavonols were the main factors affecting their coloration. The yellow-green mix petal of M. integrifolia was mainly presented by flavonols and chlorophyll, the red petal of M. punicea was presented by cyanidin, and the blue-violet mix petal of M. wilsonnii was mainly composed of a complex formed by cyanidin and other substances. Some stress resistances were also found in these three species. M. integrifolia could better maintain the stability of the transition metal ions in cells, and M. punicea showed a better ability on the defense to bacteria and dryness. Both the flowers of M. integrifolia and M. wilsonnii could better remove superoxide. Our analysis revealed the coloration mechanisms in three Meconopsis species and provided precious genetic resources for further analysis.