PnNAC03 positively regulates saponin biosynthesis and lignin accumulation during secondary cell wall formation by directly binding to the promoters of key saponin and lignin biosynthetic genes. The NAC transcription factor family plays a crucial role in the regulation of secondary metabolites biosynthesis. Saponins are the major bioactive compounds for Panax notoginseng, which is a world-globally recognized medicinal plant and possesses multiple pharmacological activities. The secondary cell wall is essential for P.notoginseng growth and stress resistance. However, the role of NAC transcription factors in regulating both saponin biosynthesis and secondary cell wall formation remains largely unknown. In this study, we characterized an NAC transcription factor, PnNAC03, which is a nuclear-localized protein and functions as a transcriptional activator. Silencing of PnNAC03 with the RNAi method in P. notoginseng calli resulted in a significant reduction in the content of saponin and the expression of key saponin biosynthetic genes, including PnSS, PnSE, and PnDS. Additionally, PnNAC03 specifically bound to the promoters of these genes, thereby enhancing their expression. Overexpression of PnNAC03 in Arabidopsis thaliana led to the increase of secondary cell wall thickness and lignin content, as well as upregulation of the expression of AtPAL and AtC4H. RNAi-mediated silencing of PnNAC03 in P. notoginseng further confirmed its role in lignin biosynthesis, as lignin content and the expression levels of PnPAL and PnC4H were significantly reduced. Furthermore, PnNAC03 could directly bind to the promoters of PAL and C4H genes in both A. thaliana and P. notoginseng. Collectively, our results highlight the dual regulatory role of PnNAC03 in promoting both saponin biosynthesis and lignin accumulation, providing valuable insights for the molecular breeding of P. notoginseng.