Mengnong sainfoin was not only a good forage crop, but also can be used as a garden ornamental and honey plant. In this study, the mutant petals from light color flower and the petals with pink color and amaranth color were used as the test materials. Based on the comprehensive analysis of petals parameters, pigment species and content to confirm the main substances affecting floral color. The result shows that: (1) the light color flower by EMS treated and the control (pink and amaranth) were three different color systems, and the light color flower was defined as yellowwhite flower according to the b^* and the h°. (2) 10 kinds of flavonoids and 5 kinds of anthocyanins were detected in 3 colors of sainfoin, but 6 varieties of kaempferol derivatives, 2 types of petunia derivatives, 2 varieties of delphinidin derivatives and 1 types of mallowin derivative were firstly reported in Mengnong sainfoin. We also found the Kaempferol3Orutinoside, Kaempferol3Oglucoside and Delphinidin3rutinoside contents were the most in 3 different color of flowers. The color change of Mengnong sainfoin was influenced by the rutin, Kaempferol3Orhamnosylrutinoside and Kaempferol3Oglucosidepcourmaric ester.