As a major source of energy, carbohydrates have a protein-saving effect. However, excessive consumption of carbohydrates can lead to the disruption of the intestinal barrier in fish, especially for carnivorous fish. Therefore, traditional Chinese medicine component Yinchenhao Decoction (YD), was used to detect the effect on intestinal barriers and microbial community equilibrium for largemouth bass in current research. In this research, a series of NC (normal carbohydrate diet) and HC (high carbohydrate diet) with graded YD treatments during 10 weeks feeding trial. Results suggested that 2% and 4% YD treatments significantly reduced gut inflammation and mucosal loss caused by HC. Compared with NC, HC significantly decreased the relative expression of intestinal tight junction-related genes (zo1, claudin1, claudin7, and occludin). However, with the application of YD, the expression of tight junction-related genes (zo1, claudin1, and claudin7) increased significantly (p < 0.05). Likewise, administration of YD significantly reduced elevated plasma diamine oxidase (DAO) activity caused by HC (p < 0.05). Additionally, YD significantly downregulated the mRNA expression of endoplasmic reticulum stress (ERS)-related genes (grp78, atf6, chopα, ire1, xbp1, and eifα) and pro-apoptosis genes (casp3, casp8, and bax) (p < 0.05), while upregulating the anti-apoptosis gene bcl2 (p < 0.05). Moreover, YD significantly increased the mRNA expression of antioxidant genes and the enzyme activities of CAT and GPX, while decreased MDA concentration significantly (p < 0.05). Whereas, YD markedly decreased the expression of pro-inflammatory genes (il1β, tnfα, il8, and nf-κB) and the immune enzymes activity (ACP and AKP) (p < 0.05) by up-regulating the expression of anti-inflammatory genes (ikb and il10). Notably, YD modulated the largemouth bass intestinal microbial community, enhanced the diversity and increased the abundance of probiotic microorganisms in the intestinal microbiota. In summary, YD supplementation in HC alleviated inflammation, apoptosis, oxidative stress, tight-junction injury, and microbiota disequilibrium in the intestine, which suggested that YD could be a valuable functional additive in aquaculture.