NAC transcription factor family protein play an important role in modulation of secondary metabolites biosynthesis. Saponins are the major bioactive compounds for Panax notoginseng which is a world-famous medicinal plant, and possess multiple pharmacological activities. Secondary cell wall play crucial roles in P.notoginseng growth and stress resistance. However, the investigations on NAC transcription factors in regulation of saponin biosynthesis and secondary cell wall formation remain elusive. In this study, we cloned and characterized a NAC transcription factor, PnNAC03, which is nuclear-localized protein and exhibits transcriptional activation activity. Inhibition of PnNAC03 with RNAi method in P. notoginseng calli resulted in a significant reduction in the content of saponin and the expression of the saponin biosynthetic genes, including PnSS, PnSE, and PnDS. Additionally, PnNAC03 was demonstrated to bind to the promoters of these genes and thereby enhancing their expression. Furthermore, overexpression of PnNAC03 in Arabidopsis thaliana led to the increase of secondary cell wall thickness and lignin content, and 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 lowered. Furthermore, PnNAC03 could directly bind to the promoters of PAL and C4H 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.