Abstract This study used 16S rDNA high-throughput sequencing to determine the effects of Jiaotai Wan on gut microflora of rats experiencing chronic unpredictable mild stress. We randomly divided 135 healthy male rats into nine groups. All groups except the control received chronic unpredictable mild stress. Rats were weighed before being subjected to sucrose preference and open field tests. Rat fecal samples were used for 16s rDNA high-throughput sequencing; the results allowed us to determine gut microfloral structure and changes. The stress treatment decreased body weight, sucrose preference, and performance in open field tests from control levels. Beta diversity of gut microflora differed across rat groups. Jiaotai Wan increased Lachnospiraceae, Bacteroides , and Akkermansia abundance, while decreasing Ruminococcaceae abundance. Therefore, Jiaotai Wan may exert antidepressant effects through regulating microbial abundance in the gut.