Chinese flavor liquor (CFL) plays an important role in Chinese culture and people’s daily lives. It is the first choice of most Chinese residents when drinking liquor, so the health problems of CFL consumption should be paid attention to. Gut microbiota plays a key role in host physiology and metabolism. Although alcohol feeding has been proved to produce evident intestinal microbial changes, most of these studies focus on pure ethanol (EtOH), and no comparative study of flavor liquor has been carried out, ignoring the role of the trace components in flavor liquor. In this study, different doses of EtOH, CFL and the extract from CFL were given to C57BL/6 mice by gastric perfusion for 3 weeks consecutively. The fecal samples were collected and the effects of EtOH, CFL and CFL extract on gut microbiota composition changes were analyzed using 16S rRNA method. Results revealed that mice fed with CFL extract had increased the richness and diversity of gut mirobiota compared to mice in normal control group. CFL extract also improved the proportion of intestinal probiotics such as Lactobacillus and Bifidobacterium. 3-weeks consumption of EtOH can alter gut bacterial communities, decrease the relative abundance of Lactobacillus, Bifidobacterium and Akkermansia, while increase the relative abundance of Clostridium in a dose-dependent manner. The effect of CFL on the composition of gut microbiota was different from that of EtOH at middle and low doses.This might be contributed to the trace components in CFL. Therefore, the effects of molecular components in CFL extract on gut microbiota deserve further investigations.