Flower color serves as a vital ornamental feature of landscape plants; Sophora japonica L. mutant ‘AM’ exhibits the different colors from the common S. japonica. ‘AM’, presenting with a light purple-red wing and keel and yellowish-white flag petals, while common S. japonica is yellow and white. The metabolites contributing to this color specificity in red-flowered S. japonica ‘AM’ are not yet fully understood. In this study, the flag, wing, and keel petals were collected from ‘AM’ at various phases, including the flower bud phase, initial flowering phase, full bloom phase, and final flowering phase, for conducting the metabolic assays targeting anthocyanins. Subsequently, we identified 45 anthocyanin-related metabolites, including nine flavonoids and 36 anthocyanins. Ten major floral chromoside metabolites were found to affect the coloration differences among the petals, where the most abundant anthocyanin was cyanidin-3-O-glucoside (Cy3G), which was much higher in the keel petal (LGB) and wing petal (YB) than in the flag petal (QB), and similarly, during the four periods of different petal types, the Cy3G content was higher in the initial flowering stage (S2), the full bloom stage (S3), and the final flowering stage (S4) than the flower bud stage (S1), which was in accordance with the trend of the observed petal floral color phenotypic difference measurement correlation. This suggested that the Cy3G accumulation was the primary factor driving the distinct coloration of varying types of petals. These findings could contribute to the understanding of the biochemical mechanisms underlying S. japonica petal coloration and may support future efforts in flower color improvement.