Objective To explore the function of short-chain dehydrogenases/reductases (SDRs) in safflower flavonoid, especially hydroxysafflower yellow A (HSYA) biosynthesis. Methods SDRs involved in HSYA biosynthesis pathway were screened based on safflower transcriptome database and metabolome database. The expression pattern was analyzed by qRT-PCR. The overexpression vector was constructed by seamless cloning technology, then genetically transformed to the Yunnan Weishan safflower strain by Agrobacterium gv3101. The transgenic T₂ generation plants were positively verified, and the gene expression of corolla SDRs was analyzed. The content of secondary metabolites was assayed by UPLC-Q-TOF/MS. Results Three SDRs genes named CtSDR1, CtSDR2 and CtSDR3 involved in HSYA biosynthesis pathway were screened. Their expression in safflower from high to low was corolla > leaf > stem > root. The expression level in corolla increased gradually with corolla development. qRT-PCR analysis of corolla with positive verification of genome insertion sequence showed that the transcription level of CtSDR3 in corolla of T₂ positive plants increased by 2~3 times compared with the blank control group, and the content of secondary metabolite HSYA increased by 7.1%~16.6% (P< 0.05). Conclusion CtSDR3 may be involved in the biosynthesis of flavonoids, especially HSYA, in safflower. It provides the support data for explaining the function of CtSDR3 in HSYA biosynthesis pathway.