OBJECTIVE: To evaluate the effects of Zhenggan Huayu decoction ((sic), ZGHY) combined with entecavir (ETV) on the gut microbiota in patients with chronic hepatitis B (CHB) fibrosis. METHODS: A total of 59 CHB-related fibrosis patients were enrolled and treated with ZGHY combined with ETV (ZGHY + ETV) and ETV alone. Fecal samples were collected from patients at weeks 0, 12, and 24 after treatment and gut microbiota were analyzed by 16S rRNA gene sequencing. RESULTS: Compared to the ETV group, microbiota diversity in the ZGHY + ETV group was increased after 24 weeks. Some potentially pathogenic bacteria, including Fusobacteriaceae spp., Acidaminococcus spp., and Erysipelotrichaceae spp. were reduced in the ZGHY + ETV group, while Eubacteriaceae spp., Lactococcus spp., and several other beneficial bacteria were increased. CONCLUSION: Decreases in pathogenic bacteria and increases in probiotics were not always observed in the Traditional Chinese Medicine (TCM) group (e.g., Rothia was abundant). As an adjuvant TCM formulation for ETV, ZGHY had a positive role in the treatment of CHB patients.