Narcissus is widely used for cut flowers and potted plants, and is one of the most important commercial bulbous flowers in the floricultural industry. In this study, ten carotenoid and eighteen flavonoid compounds from the perianths and coronas of fifteen narcissus cultivars were measured by HPLC-APCI-MS/MS and UPLC-Q-TOF-MS/MS. Among these, six carotenoids, a total of seventeen flavonols and chlorogenic acid were identified in narcissus for the first time. A multivariate analysis was used to explore the relationship between flower color and pigment composition. We found that all-trans-violaxanthin and total carotenoid content were the main factors that affected flower color. These investigations could provide a global view of flower color formation and a theoretical basis for hybridization breeding in narcissus.