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<i>Sophora japonica</i> L. is an important landscaping and ornamental tree species throughout southern and northern parts of China. The most common color of <i>S. japonica</i> petals is yellow and white. In this study, <i>S. japonica</i> flower color mutants with yellow and white flag petals and light purple-red wing and keel petals were used for transcriptomics and metabolomics analyses. To investigate the underlying mechanisms of flower color variation in <i>S. japonica</i> ‘AM’ mutant, 36 anthocyanin metabolites were screened in the anthocyanin-targeting metabolome. The results demonstrated that cyanidins such as cyanidin-3-O-glucoside and cyanidin-3-O-rutinoside in the ‘AM’ mutant were the key metabolites responsible for the red color of the wing and keel petals. Transcriptome sequencing and differentially expressed gene (DEG) analysis identified the key structural genes and transcription factors related to anthocyanin biosynthesis. Among these, <i>F3′5′H</i>, <i>ANS</i>, <i>UFGT79B1</i>, <i>bHLH</i>, and <i>WRKY</i> expression was significantly correlated with the cyanidin-type anthocyanins (key regulatory factors affecting anthocyanin biosynthesis) in the flag, wing, and keel petals in <i>S. japonica</i> at various flower development stages.