Rosa rugosa is a deciduous shrub belonging to Rosa L. in Rosaceae. It has a high ornamental value and commercial value, but its single color limits the development and utilization of rose and its application in landscape architecture. In order to explore the coloring substances of three different varieties of roses, ‘Rosa rugosa × Rosa sertata’, ‘Rosa Crimson Glory’ and ‘Rosa alba’, this study used ultra-high performance liquid chromatography-quadrupole-time-of-flight mass spectrometry (UPLC-Q-TOF-MS) to detect the types and contents of flavonoids in petals. The KEGG database was used to enrich the differential metabolites, screen out the key metabolites, and analyze the correlation with the phenotypic value of flower color. The results were as follows: (1) A total of 58 metabolites were detected in the petals of three different color rose varieties, of which only one anthocyanin was cyanidin-3-O-glucoside, accounting for 30.45%. (2) K-means clustering analysis showed that a total of 12 key metabolites were annotated to the KEGG metabolic pathway. Among them, pinocembrin and myricetin were the main substances that determined the red color of ‘Rosa rugosa × Rosa sertata’ and ‘Rosa Crimson Glory’, and eriodictyol, luteolin and kaempferol were the main substances that determined the white color of ‘Rosa alba’. In conclusion, this study can provide a theoretical basis for the breeding of roses with specific colors and promote the application of roses in landscaping.