Aster tataricus (L.) is an important medicinal plant in China. Its roots are rich in flavonoids, the main medicinal components. However, the molecular basis of flavonoid biosynthesis in the roots of A. tataricus remains unclear. In this study, the content of total flavonoid of A. tataricus roots at different developmental stages was measured first, and the results showed that the content of total flavonoid gradually decreased from September to November, which may be caused by the stagnation of A. tataricus growth due to the decrease in temperature after September. Then, an integrated analysis of transcriptome and metabolome was conducted on five developing stages of A. tataricus roots to identify flavonoid compositions and potential genes involved in flavonoid biosynthesis. A total of 80 flavonoid metabolites, of which 75% were flavonols and flavonoids, were identified in metabolomic analyses, among which isorhamnetin, kaempferol, quercetin, and myricetin were the main skeletons of these flavonoids. Cluster analysis divided these 80 flavonoids into 3 clusters. The compounds in cluster I mainly accumulated in S1, S3, and S5. In cluster II, the relative content of the flavonoid metabolites showed an upward trend from S2 to S4. In cluster III, the flavonoids decreased from S1 to S5. A total of 129 structural genes, including 43 PAL , 23 4CL , 9 C4H , 4 CHS , 18 CHI , 3 F3H , 5 F3’H , 1 F3′5′H , 21 FLS , and 2 FSII , and 65 transcription factors, including 22 AP2/ERF , 7 bHLH , 5 bZIP , 8 MYB , 11 NAC , and 12 WRKY , showed significant correlation with total flavonoid content. Eighteen genes (7 4CL , 5 C4H , 2 CHI , 1 F3H , and 3 FLS ) and 30 genes (5 PAL , 9 4CL , 1 C4H , 2 CHI , 1 F3H , 1 DFR , 7 3AT , 1 BZ1 , and 3 UGT79B1 ) were identified as key structural genes for kaempferol and anthocyanins biosynthesis, respectively. Our study provides valuable information for understanding the mechanism of flavonoid biosynthesis in A. tataricus root. Supplementary Information The online version contains supplementary material available at 10.1007/s10265-022-01426-4.