Spatholobus suberectus Dunn is rich in flavonoids, which were previously demonstrated to respond to changing light conditions. In this study, through weighted gene co-expression network analysis (WGCNA), MYB genes were screened as the potential regulator for these light-intensity-induced changes. One MYB gene, SsMYB106, was chosen for in-depth research. Analysis showed that SsMYB106 was an R2R3-type MYB transcription factor, regulated by light, and involved in controlling the light responses of S. suberectus. SsMYB106 was then transiently overexpressed in S. suberectus flowers and stably overexpressed in Nicotiana benthamiana Domin. SsMYB106 overexpression promoted flavonoids (especially catechins) accumulation, and affected expressions of all the flavonoid biosynthetic pathway genes. In transient overexpression, SsDFR1 was the only significantly decreased gene, while other 17 genes were significantly increased. In stable overexpression, nearly all genes were upregulated or at least unchanged. SsMYB106 overexpression also might function in inhibiting anthocyanin and lignin biosynthesis. This study deepens our understanding of SsMYBs gene functions in regulating and enhancing flavonoids, and would be beneficial for designing high-valued S. suberectus in future.