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<i>Angelica dahurica</i> var. <i>formosana</i> (<i>ADF</i>), which belongs to the Umbelliferae family, is one of the original plants of herbal raw material Angelicae Dahuricae Radix. <i>ADF</i> roots represent an enormous biomass resource convertible for disease treatment and bioproducts. But, early bolting of <i>ADF</i> resulted in lignification and a decrease in the coumarin content in the root, and roots lignification restricts its coumarin for commercial utility. Although there have been attempts to regulate the synthesis ratio of lignin and coumarin through biotechnology to increase the coumarin content in ADF and further enhance its commercial value, optimizing the biosynthesis of lignin and coumarin remains challenging. Based on gene expression analysis and phylogenetic tree profiling, <i>AdNAC20</i> as the target for genetic engineering of lignin and coumarin biosynthesis in <i>ADF</i> was selected in this study. Early-bolting <i>ADF</i> had significantly greater degrees of root lignification and lower coumarin contents than that of the normal plants. In this study, overexpression of <i>AdNAC20</i> gene plants were created using transgenic technology, while independent homozygous transgenic lines with precise site mutation of <i>AdNAC20</i> were created using CRISPR/Cas9 technology. The overexpressing transgenic ADF plants showed a 9.28% decrease in total coumarin content and a significant 12.28% increase in lignin content, while knockout mutant plants showed a 16.3% increase in total coumarin content and a 33.48% decrease in lignin content. Furthermore, 29,671 differentially expressed genes (DEGs) were obtained by comparative transcriptomics of OE-<i>NAC20</i>, KO-<i>NAC20</i>, and WT of <i>ADF</i>. A schematic diagram of the gene network interacting with <i>AdNAC20</i> during the early-bolting process of <i>ADF</i> was constructed by DEG analysis. <i>AdNAC20</i> was predicted to directly regulate the transcription of several genes with SNBE-like motifs in their promoter, such as MYB46, C3H, and CCoAOMT. In this study, <i>AdNAC20</i> was shown to play a dual pathway function that positively enhanced lignin formation but negatively controlled coumarin formation. And the heterologous expression of the <i>AdNAC20</i> gene at <i>Arabidopsis thaliana</i> proved that the <i>AdNAC20</i> gene also plays an important role in the process of bolting and flowering.