The root of Angelica sinensis is one of the most widely used of traditional Chinese medicines. In the commercial planting, bolting and flowering (BF) for ca. 40% of two‐year‐old plants reduce root yield and quality. Although changes in physiology in bolted plants have been investigated, the mechanism for activating BF has not been identified. ●Here, transcriptomics profiles at four different growth stages (S1 to S4) were performed, genes expression were validated by qRT‐PCR, and the accumulations of endogenous hormones were quantified by HPLC. ●A total of 60,282 unigenes were generated with 2,282, 1,359 and 2,246 differentially expressed genes (DEGs) observed at S2 vs S1, S3 vs S2 and S4 vs S3, respectively; and 558 genes co‐existing at least three stages from S1 to S4 were obtained. Functional annotation classified 38 DEGs linked with flowering pathways including: photoperiodism, hormone signaling, carbohydrate metabolism and floral development. The levels of genes expression as well as hormones (GA1, GA4 and IAA) and soluble sugar were consistent with the BF. ●It can be concluded that the BF of A. sinensis is controlled by multiple genes. This integrated analysis of transcriptomics together with targeted hormones and soluble sugar provides new insights into the regulation of BF of A. sinensis.