bHLHtranscription factors are involved in multiple aspects of plant biology, such as the response to abiotic stress.Erigeron breviscapusis a composite plant, and its rich flavonoids have strong preventive and therapeutic effects on cardio cerebral vascular disease.EbbHLH80, a gene fromE. breviscapusthat positively regulates flavonoid synthesis, was previously characterized. However, it is unclear whetherEbbHLH80increases flavonoid accumulation, which affects salt tolerance. The function ofEbbHLH80in transgenic tobacco seeds was identified by phylogenetic analysis and metabolome-transcriptome analysis. We investigated the role ofEbbHLH80in salt stress response. Our results showed that the expression ofEbbHLH80increased following salt treatment. Integrating the metabolome and transcriptome analysis ofEbbHLH80-OE and Yunyan 87 (WT) seeds, we identified several genes and metabolites related to flavonoid biosynthesis and salt stress. Moreover,EbbHLH80-OE plants displayed higher salt tolerance than wild-type plants during seed germination and seedling growth. After salt treatment, transgenic tobacco had significantly lower levels of reactive oxygen species (ROS) than WT, with enhanced levels of antioxidant enzyme expression. Altogether, our results demonstrated thatEbbHLH80might be a positive regulator, promoting salt tolerance by modulating ROS scavenging and increasing stress-responsive genes.