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Non‐alcoholic fatty liver disease (NAFLD) is a chronic liver disease with high rates of occurrence. Research has found that NAFLD patients experience varying degrees of intestinal flora imbalance. There is evidence that traditional Chinese medicine (TCM) positively regulates imbalances in the gut microbiota caused by liver diseases. Jiangan‐Jiangzhi pill (JGJZ) is a common Chinese remedy that can treat NAFLD clinically. This article investigates how JGJZ affects NAFLD and assesses related changes in the intestinal flora. We established a NAFLD rat model by feeding them a high‐fat diet (HFD) and gave different interventions. After twelve weeks, the results revealed that JGJZ decreased the total cholesterol, triglyceride, alanine aminotransferase, and aspartate aminotransferase in the serum of NAFLD rats. Histopathological staining demonstrated that JGJZ relieved cellular fat accumulation in the liver. Inflammatory cytokine levels (IL‐6, IL‐1β, and TNF‐α) were down‐regulated. Analysis of 16S rRNA demonstrated that JGJZ changed the community compositional structure of gut microbiota, characterized by a decrease in the Firmicutes‐to‐Bacteroidetes ratio, and increased gut microbiota diversity and the abundance of dominant groups. Accordingly, our study illustrated that JGJZ exerted a better effect in treating HFD‐induced NAFLD, which may be closely related to ameliorating gut microbiota dysbiosis.