Background. Clinacanthus nutans (Burm.f.) Lindau (C. nutans) has been used in the therapy of hepatitis B (HB) and is effective; however, the mechanism of action has not been elucidated. Objective. To investigate the protective effects of C. nutans aqueous extract on the hepatitis B virus (HBV) mouse model based on correlation analysis between gut microbiota and liver metabolomics. Materials and Methods. We firstly constructed the animal model by high-pressure injection of pcDNA3.1(+)/HBV plasmid into the tail vein and treated it with C. nutans. The biomarkers and inflammatory cytokines of HB were detected by enzyme-linked immunosorbent assay and quantitative PCR; the Illumina-MiSeq platform was used for investigating gut microbiota; the LC-MS/MS method was utilized on screening liver tissue metabolites; multiomics joint analysis was performed using the R program. Results. Compared with the modeling group, C. nutans significantly decreased the expression levels of HBsAg, IL-1β, TNF-α P < 0.05 in the serum, and cccDNA P < 0.05 in the liver tissues of mice. C. nutans dramatically reduced the ratio of Firmicutes and Bacteroidetes P < 0.05 and significantly declined the proportion of Lactobacillaceae and Lactobacillus P < 0.05 , dramatically increasing the relative abundance of Bacteroidales_S24-7_group, Rikenellaceae, and Alistipes P < 0.05 ; LC-MS/MS analysis results showed that C. nutans dramatically upregulate hippuric acid, L-histidine, trehalose, D-threitol, and stachyose and downregulate uridine 5′-diphosphate, cholic acid, trimethylamine N-oxide, CDP-ethanolamine, and phosphorylcholine P < 0.05 . The correlation analysis revealed that C. nutans affects the related metabolite levels of hippuric acid and cholic acid through the modulation of crucial bacteria (Alistipes) P < 0.01 , exerting specific anti-inflammatory effects. Conclusion. These results suggest that C. nutans exerts protective effects in HBV model mice, showing the therapeutic potential for anti-HBV infection.