Chinese baijiu, an ancient fermented alcoholic beverage, contains ethanol and a variety of compounds. One of the most popular types of Chinese baijiu is Jiang-flavor baijiu. To investigate the effects of Jiang-flavor baijiu on organ function and gut microbiota, we developed a moderate drinking mouse model and studied its effects on the liver, kidney biomarkers, memory function, and gut microbiota. The results showed that ethanol caused more hepatic steatosis, liver and kidney damage, and memory impairment than Jiang-flavour baijiu consumption. Furthermore, Jiang-flavor baijiu altered the gut microbiota by increasing the abundance of beneficial taxa such as Lactobacillus and Akkermansia, whereas ethanol increased the abundance of harmful bacteria such as Prevotella and Mucispirillum. Our findings provide preliminary evidence that moderate dose Jiang-flavor baijiu regulates gut microbiota and organ function and provide a theoretical foundation for future research on the positive health effects of particular varieties of Chinese baijiu.