Background: Recently, several studies reported that transplanting stool from depressed patients could induce depression-like behaviors in mice. In addition, antidepressants presented not only antidepressant effects, but also antibacterial effects in those animals. Therefore, this study firstly investigated on the changes of gut microbiota in depressed patients under effective antidepressant treatment.Methods: We recruited 30 patients with drug-naive first-episode MDD (Patients group) and 30 healthy controls (Control group), and collected their stool samples to complete 16S rRNA sequencing. Next, Patients group received 20 mg/d of escitalopram. After the symptoms improved, the feces of Patients group were collected and marked as Follow-up group to complete sequencing for the second time. We then investigated into the differences of gut microbiota between patients (Patients and Follow-up groups) and controls (Control group), the characteristics of gut microbiota under treatment, and the potential differences in metabolic functions. Results: A significant difference in gut microbiota abundance was found after escitalopram treatment. The Firmicutes/Bacteroides ratio significantly decreased in the Follow-up group. After treatment, the species diversity of gut microbiota tended to be back to normal state in Follow-up group. The mainly difference of metabolic function were found as follows: Transport and catabolism, Nervous system, Glycan biosynthesis and metabolism.Conclusions: Under escitalopram treatment, the gut microbiota diversity of MDD patients tended to back to normal state. However, several structures and metabolic pathways in microbes remained differences between patients and controls, which might be related to the relapse of MDD.