Chinese herbal medicines have become a new green feed additive in the aquaculture industry. The aim of this study is to investigate the effects of traditional Chinese herbal medicines (Isatidis radix, Forsythia suspensa, and Schisandra chinensis) on the growth performance, antioxidant capacity, and intestinal microbiota of hybrid snakehead (Channa maculata ♀ × Channa argus ♂). A total of 600 fish (mean weight: 15.85 ± 0.15 g) were randomly assigned to five groups, including the control group (CG), I. radix extract group (IRE), F. suspensa extract group (FSE), S. chinensis extract group (SCE), and the Chinese herbal medicine mixture group (CHMM; a mixture of extracts of I. radix, F. suspensa, and S. chinensis at the ratio of 1:1:1) for 6 weeks. The results show that the IRE-supplemented diet improved the survival rate (SR), feed efficiency ratio (FE), and condition factor (CF) compared to others. Compared to the control group, the activity of superoxide dismutase (SOD) in plasma and intestine was significantly increased in the FSE and CHMM groups, whereas the content of malondialdehyde (MDA) in plasma and liver was significantly reduced in the SCE group. A 16s rRNA analysis indicates that dietary supplementation with FSE significantly promoted the proliferation of Fusobacteriota, while IRE supplementation increased the alpha diversity of intestinal bacteria. In conclusion, the addition of I. radix to the diet of hybrid snakehead improves growth, antioxidant capacity, and liver and intestine health, and modulates the intestinal microbiota of snakehead positively.