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Transcription factors play crucial roles in regulating plant abiotic stress responses and physiological metabolic processes, which can be used for plant molecular breeding. In this study, an R2R3-MYB transcription factor gene, <i>AtMYB12</i>, was isolated from <i>Arabidopsis thaliana</i> and introduced into <i>Salvia miltiorrhiza</i> under the regulation of the CaMV35S promoter. The ectopic expression of <i>AtMYB12</i> resulted in improved salt tolerance in <i>S. miltiorrhiza</i>; transgenic plants showed a more resistant phenotype under high-salinity conditions. Physiological experiments showed that transgenic plants exhibited higher chlorophyll contents, and decreased electrolyte leakage and O₂⁻ and H₂O₂ accumulation when subjected to salt stress. Moreover, the activity of reactive oxygen species (ROS)-scavenging enzymes was enhanced in <i>S. miltiorrhiza</i> via the overexpression of <i>AtMYB12</i>, and transgenic plants showed higher superoxide dismutase (SOD), catalase (CAT), and peroxidase (POD) activities compared with those of the wild type (WT) under salt stress, coupled with lower malondialdehyde (MDA) levels. In addition, the amount of salvianolic acid B was significantly elevated in all <i>AtMYB12</i> transgenic hair roots and transgenic plants, and qRT-PCR analysis revealed that most genes in the phenolic acid biosynthetic pathway were up-regulated. In conclusion, these results demonstrated that <i>AtMYB12</i> can significantly improve the resistance of plants to salt stress and promote the biosynthesis of phenolic acids by regulating genes involved in the biosynthetic pathway.