Gut microbiota dysbiosis has been implicated as a vital element in the development or exacerbation of mental disorders, such as major depressive disorder (MDD). Based on the current interest in the gut-brain axis, we investigate the effects of chlorogenic acid (CGA) on gut microbiota in a rat model of MDD. Depression was induced by the adrenocorticotropic hormone (ACTH, 100 μg per rat) in male Wistar rats, which were intervened with using saline or CGA (500 mg kg-1). Behavioral changes and serum parameters were assessed and fecal samples were analyzed by 16S rRNA gene sequencing. Our studies demonstrated that CGA pretreatment ameliorated depression-like behavior (SPT, FST, TST, and OFT) and serum biochemical levels (5-HT, DA, IL-6, and TNF-α) in ACTH-induced depression rats. In addition, CGA ameliorated the decrease in fecal microbiota diversity in ACTH-treated rats. In particular, at the genus level, the changes in the relative abundance of some key bacteria such as Desulfovibrionales, Desulfovibrio, Klebsiella, Burkholderiales, and Bifidobacterium were modulated by CGA pretreatment. These results indicated that CGA could modify the gut microbial community structure, which may contribute to its antidepressant effects.