Intestinal bacterial β-glucuronidases, the key enzymes responsible for the hydrolysis of various glucuronides into free aglycone, have been recognized as key targets for treating various intestinal diseases. This study aimed to investigate the inhibitory effects and mechanisms of the Mulberry bark constituents on E. coli β-glucuronidase (EcGUS), the most abundant β-glucuronidases produced by intestinal bacteria. The results showed that the flavonoids isolated from Mulberry bark could strongly inhibit E. coli β-glucuronidase, with IC50 values ranging from 1.12 µM to 10.63 µM, which were more potent than D-glucaric acid-1,4-lactone. Furthermore, the mode of inhibition of 5 flavonoids with strong E. coli β-glucuronidase inhibitory activity (IC50 ≤ 5 µM) was carefully investigated by a set of kinetic assays and in silico analyses. The results demonstrated that these flavonoids were noncompetitive inhibitors against E. coli β-glucuronidase-catalyzed 4-nitrophenyl β-D-glucuronide hydrolysis, with Ki values of 0.97 µM, 2.71 µM, 3.74 µM, 3.35 µM, and 4.03 µM for morin (1: ), sanggenon C (2: ), kuwanon G (3: ), sanggenol A (4: ), and kuwanon C (5: ), respectively. Additionally, molecular docking simulations showed that all identified flavonoid-type E. coli β-glucuronidase inhibitors could be well-docked into E. coli β-glucuronidase at nonsubstrate binding sites, which were highly consistent with these agents' noncompetitive inhibition mode. Collectively, our findings demonstrated that the flavonoids in Mulberry bark displayed strong E. coli β-glucuronidase inhibition activity, suggesting that Mulberry bark might be a promising dietary supplement for ameliorating β-glucuronidase-mediated intestinal toxicity.