Forty 3-week-old Kunming mice were randomly divided into 4 groups infected four dose amount(low, medium, high dose and the control) of flavonoids from Scutellaria baicalensis respectively to study its effects on the mice. The mice of control group(CON) were given 0.9% sodium chloride solution every day, while the mice of flavonoids from Scutellaria baicalensis low-dose(HQHTL), medium-dose(HQHTM) and high-dose(HQHTH) groups were intragastrically injected with 25, 50 and 100 mg/kg flavonoids from Scutellaria baicalensis solution every day, respectively. After 28 days of intragastrically injected, the growth performance, antioxidant capacity, microbial diversity and community composition of cecum were collected in the study. The results showed that compared with CON, the average daily gain mass of mice were significantly(P<0.05) increased, serum total superoxide dismutase activities of mice were significantly(P<0.05) or extremely significantly(P<0.01) increased, and malondialdehyde levels were significantly(P<0.05) or extremely significantly(P<0.01) decreased in the treated groups. The Sobs and Bootstrap indexes of cecum microorganisms of HQHTM and HQHTH mice were significantly(P<0.05) decreased, and their Chao and Ace indexes were extremely significantly(P<0.01) decreased. The relative abundances of Actinobacteriota of HQHTM and HQHTH mice were significantly(P<0.05) increased, and the relative abundances of their Verrucomicrobiota were significantly(P<0.01) increased. The relative abundance of Deferribacterota of HQHTH mice were significantly(P<0.01) decreased, and the relative abundances of Deferribacterota of HQHTL and HQHTM mice were significantly(P<0.05) decreased. The relative abundances of Norank_f__Ruminococcaceae and Prevotella in the cecum of mice treated with flavonoids from Scutellaria baicalensis were significantly(P<0.05) decreased. The relative abundance of Anaerotruncus in the cecum of HQHTL and HQHTM mice were significantly(P<0.05) decreased, while the relative abundances of Akkermansia in the cecum of HQHTM and HQHTH mice were significantly(P<0.01) increased. In conclusion, flavonoids from Scutellaria baicalensis could improve the growth performance and the antioxidant function of mice and regulate the microflora of mice’s cecum. The treated dose 50 mg/kg flavonoids could yield better effects on growth.