Background Non-alcoholic fatty liver disease (NAFLD) is a frequently occurring clinical disease, which could be treated by traditional Chinese medicine. However, the effects and mechanisms of xiao-zhi-fang (XZF) alone or in combination with fructooligosaccharides (FOS) on NAFLD remains unclear. Methods This study established the NAFLD mouse model by feeding with a high-fat diet and by administering with XZF and/or FOS. Moreover, the fat content in the liver tissues was evaluated by oil red O and hematoxylin and eosin staining, and the liver function indices were examined using a biochemical analyzer. Changes in the intestinal flora were monitored using 16S rRNA gene sequencing. The results of the current study showed that the alanine aminotransferase, aspartate aminotransferase, total triglyceride, total cholesterol levels, and the amount of lipid accumulation were markedly elevated in NAFLD mice. Results XZF alone or in combination with FOS significantly reduced lipid accumulation in the liver and blood lipid levels in NAFLD mice. Moreover, XZF alone or in combination with FOS notably altered the intestinal flora structure in NAFLD mice. Consequently, 17 operational taxonomic units were decreased and nine were increased in the XZF and/or FOS groups. Conclusions FOS may accelerate the intestinal microecological balance in NAFLD mice after treatment with XZF by promoting intestinal flora growth, thereby enhancing the therapeutic effect of XZF on NAFLD.