[Objective] This study aims to analyze the composition and difference of flavonoid metabolites in yellow, milky white and white petals of cotton, which provides theoretical basis for the further research and utility of pigmentation in cotton flower. [Method] In this study, firstly, the Ultra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) detection platform and Analyst 1.6.3 were employed to analyze the flavonoids in three types of cotton petals from Hai 7124(yellow flower), TM-1 (milk white flower), and Shixiya 1 (white flower). Then the multivariate statistical analysis was used to analyze different metabolites. Finally, KEGG and K-means was used to investigate the synthetic pathways of different metabolites. [Result] A total of 184 types of flavonoid metabolites were detected in petals of three colors, among which 76 were flavonol (accounting for 41.30%) and 51 were flavone (accounting for 27.72%). And 171 different metabolites were obtained, which were significantly enriched in the biosynthetic pathway of flavone and flavonols and the biosynthetic pathway of flavonoids. By analyzing the relative content of flavonoids metabolites in yellow, milky white and white petals, 15 different metabolites were found to show an increasing trend and 15 metabolites content were decreasing. Among them, 5 metabolites were annotated in the known KEGG pathway, and the content of chrysoeriol, astragalin and rutin were all increased in the biosynthesis pathway of flavone and flavonoid. In addition, in flavonoid biosynthesis pathway, the content of aromadendrin and epicatechin increased, and the content of isosalipurposide were decreased. [Conclusion] Different flavonoid metabolites in the three cotton materials were found to be mainly involved in the biosynthesis pathway of flavone and flavonol as well as the biosynthesis pathway of flavonoids. As the content of isoaridin was decreased gradually in yellow, milky white and white petals, we speculate that this substance was related to the formation of yellow cotton petals.