This study aims to explore the mechanism of biogas slurry effect on the quality formation of Astragalus membranaceus (Fisch.) Bge. var. mongholicus (Bge.) Hsiao. One year old A. membranaceus seedlings were used as the experimental material. Using a large field experiment, three treatments, namely, the optimized treatment of biogas slurry (BS), conventional fertilizer (CF) and clear water treatment (CK), were set up to investigate the changes in the contents of total flavonoids (TAF) and total saponins (TANS) in roots, biomass and physiological characteristics in roots and leaves. And the transcriptome of A. membranaceus in different treatments was also analyzed. Results showed that compared with CK and CF treatments, BS treatment significantly increased the plant height (PH) and root dry weight (DWT) of A. membranaceus, increased the activities of peroxidase (POD), catalase (CAT) and ascorbic acid peroxidase (APX) and the contents of free proline (Pro), soluble sugar (SS), and soluble protein (SP), as well as promoted the contents accumulation of TAF and TANS. Transcriptome analysis revealed that the number of differentially expression genes (DEGs) between the BS and CK treatment groups amounted to 1 755. The DEGs of BS and CF treatments were 519. DEGs were mainly clustered into biological processes such as flavonoids, terpenoids, 2-hydroxyisoflavone reductase and phenylpropane biosynthesis, as well as in molecular functions related to starch, sucrose metabolism, redox activity, and phytohormone signaling pathways, etc. And most of the relevant DEGs in each pathway were mainly up-regulated. APF7, WRKY44, GGT3, CHS, HMGS and UGT73C5 genes may be involved in the process of improving quality of A. membranaceus by biogas slurry. Correlation analysis showed highly significant positive correlations between CHS, HMGS, ARF7, WRKY44 and APX, CAT, TAF, SP, POD, SS, UGT73C5. Similarly, there were significant positive correlations between UGT73C5 and DWT. This study indicated that biogas slurry can regulate the biomass, physiology and active ingredient biosynthesis of A. membranaceus to promote the formation of its quality.