MeJA can help plants resist external stress, and waterlogging stress is the most serious stress for safflower. The mechanism by which MeJA (Methyl jasmonate) induction helps safflower resist waterlogging stress is unclear. Our results indicate that CtMYB63 responds to MeJA through the TGACG motif element, and MeJA induction can further increase the expression of CtMYB63. Under MeJA induction, CtMYB63 is expressed by regulating the transcriptional expression of CtDFR1, CtANS1 and CtANR1, thereby increasing the biomass and flavonoid content of safflower, but inhibiting plant elongation. Our waterlogging stress experiments further demonstrated that overexpression of CtMYB63 can enhance antioxidant enzyme activity to clear the accumulation of MDA (Malondialdehyde), H