Astragalus membranaceus is a model of traditional ‘homologous nature of medicine and food’. Its stems and leaves have been proven to have a variety of biological activities. In this study, high-throughput sequencing technology was used to sequence transcriptomics and metabolomics A. membranaceus stems and leaves at different growth stages (flowerless stage, flower bud stage, flowering stage, green fruit stage, mature fruit staged, and withering stage), and a regulation analysis was conducted on its differentially expressed genes and differentially accumulated metabolites. The results showed that five hub genes, PAL, CHI, AMIE, CAD, and PRX, were found to play a central regulatory role in flavonoid biosynthesis. The combined analysis of transcriptomics and metabolomics constructed a flavonoid metabolic regulatory network during the growth and development of A. membranaceus stems and leaves. At the same time, based on the significant antioxidant activity of isoquercitrin, three genes that may be related to isoquercitrin biosynthesis were screened, namely IF7MAT, FG3, and UGT78D2. The results of this study provide insights into the biosynthesis and comprehensive development and utilization of flavonoids in A. membranaceus.