Abstract: 【Objective】 The aim of the study was to compare the flavonoid metabolic networks of wild and cultivated Taxus cuspidata Sieb. et Zucc. species，deeply analyze the secondary metabolic evolution pattern of Taxus cuspidata Sieb. et Zucc. and the metabolic network of medicinal plants， which could provide reference basis for the selection of high-quality varieties of Taxus cuspidata Sieb. et Zucc. with targeted enrichment of medicinal active components.【Method】 Two wild Taxus cuspidata Sieb. et Zucc. species from Dandong，Liaoning（W1）and Wangqing，Jilin（W2） and three cultivated species Taxus cuspidata var. nana（C1），Taxus cuspidata Sieb. et Zucc.×Taxus cuspidata var. nana cuspidata var. nana hybrid（C2），and golden yew（C3） were used as research object. Metabolomics and transcriptomics analysis were conducted on the young leaves of wild and cultivated Taxus cuspidata Sieb. et Zucc. species， and principal component analysis （PCA） was performed on the metabolites in the samples. The relative concentrations of metabolites in the samples were detected by liquid chromatography-tandem mass spectrometry （LC-MS/MS）. Based on Illumina Novaseq 6000 platform， differentially expressed genes （DEGs） were screened according to the criteria of P<0.05 and fold change≥1.5. KEGG metabolic pathway enrichment analysis was conducted for the metabolites. The flavonoid biosynthesis pathway network was constructed through the combined analysis of metabolomics and transcriptomics， and the transcriptional sequencing data of key genes were verified by real-time fluorescence quantitative PCR.【Result】 Wild and cultivated Taxus cuspidata Sieb. et Zucc. species showed highly clear group-specific separation in metabolite composition，with principal component 1 （PC1） and principal component 2 （PC2） explaining 54.2% and 22.2% of the variation respectively. KEGG metabolic pathway enrichment analysis results showed that there were significant difference in the metabolite spectra between the cultivated and wild Taxus cuspidata Sieb. et Zucc. species comparison groups. These differences were observed in five major categories： metabolism， human diseases， biological systems， environmental information processing， and cellular processes. The top 20 enriched metabolic pathways included 11， 4， 3， 1， and 1 pathways respectively； in the metabolism category， the enriched metabolic pathways included isoflavone biosynthesis， steroid hormone biosynthesis， and flavonoid biosynthesis. Compared with the wild resources， the cultivated Taxus cuspidata Sieb. et Zucc. species significantly enriched the pathways related to secondary metabolites mainly composed of flavonoids， which were involved in nutrient and morphogensis. The distribution quantity of DEGs showed a polarized pattern in different comparison groups. Among them， the number of DEGs obtained in the W2 vs C1 comparison group was the largest （851）， accoun-ting for 50.38%； followed by W1 vs C1 comparison group （491）， accounting for 29.07%. The highly expressed cluster DEGs of the cultivated Taxus cuspidata Sieb. et Zucc. species enriched genes related to plant growth and development regulation， nutrient accumulation and transport， organ development and morphological formation， quality improvement， and hormone signal transduction for promoting growth； while the highly expressed cluster DEGs of the wild Taxus cuspidata Sieb. et Zucc. species enriched genes related to environmental perception， efficient resource utilization， reproductive strategy regulation， interspecific competition， and multiple resistances. There were great difference in the relative concentrations of flavonoid substances between the cultivated and wild Taxus cuspidata Sieb. et Zucc. species. Except for naringenin-7-O-glucoside， the relative concentrations of the other six flavonoid substances were significantly higher in the three cultivated Taxus cuspidata Sieb. et Zucc. species than in the two wild Taxus cuspidata Sieb. et Zucc. species （P<0.05， the same below）. There are great difference in the expression of key genes in the phenylalanine to flavonoid metabolic pathway between the wild and cultivated Taxus cuspidata Sieb. et Zucc. species. Among cytochrome P450 family genes， the expression level of the cultivated Taxus cuspidata Sieb. et Zucc. species CYP75A3 gene was lower than that of wild Taxus cuspidata Sieb. et Zucc. species， while the expression level of the cultivated Taxus cuspidata Sieb. et Zucc. species CYP75B137 gene was higher than that of wild Taxus cuspidata Sieb. et Zucc. species. Compared with the wild Taxus cuspidata Sieb. et Zucc. species， the expression levels of genes related to R2R3-MYB， bHLH， and WD40 transcription factors were significantly up-regulated in the cultivated Taxus cuspidata Sieb. et Zucc. species. The results of real-time fluorescence quantitative PCR for nine genes were consistent with the transcriptome sequencing data.【Conclusion】 Artificial cultivation and domestication directionally reshape the flavonoid metabolic network of Taxus cuspidata Sieb. et Zucc. Cultivated Taxus cuspidata Sieb. et Zucc. species form an efficient metabolic flux pattern through enhanced upstream supply + branch-point regulation + coordinated MBW transcriptional control，thereby promoting the targeted accumulation of functional flavonoids，whereas wild Taxus cuspidata Sieb. et Zucc. maintain greater flavonoid structural diversity to support broad adaptation to complex environmental stresses.