Color fading caused by a decrease in anthocyanin accumulation during the post-flowering stage significantly affects postharvest quality of chrysanthemum. However, the underlying mechanism by which anthocyanin accumulation decreases during the post-flowering stage still unclear, which greatly restricts design of molecular breeding in chrysanthemum. Here, a chrysanthemum SG7 R2R3 MYB transcription factor (TF), CmMYB3-like, was identified to have a function in regulating anthocyanin biosynthesis during the post-flowering stage. Quantitative real time PCR (qRT-PCR) assays showed that the expression of CmMYB3-like was gradually downregulated when anthocyanin content increased during the flowering stage and was significantly upregulated during the post-flowering stage. Genetic transformation of chrysanthemum and dual-luciferase assays in N. benthamiana leaves showed that CmMYB3-like suppressed anthocyanin accumulation by inhibiting the transcription of CmCHS and CmANS directly and that of CmF3H indirectly. However, overexpression or suppression of CmMYB3-like did not affect the biosynthesis of flavones or flavonols. Genetic transformation of chrysanthemum revealed that the overexpression of CmMYB3-like inhibited anthocyanin accumulation, but its suppression prevented the decrease in anthocyanin accumulation during the post-flowering stage. Our results revealed a crucial role of CmMYB3-like in regulating the color of petals during the post-flowering stage and provided a target gene for molecular design breeding to improve the postharvest quality of chrysanthemum.