PURPOSE: To explore the related mechanisms of electroacupuncture at the "Siguan" acupoints in treating post-stroke depression (PSD). METHODS: Fifty male SD rats were randomly divided into the blank group, stroke group, PSD group, Siguan group and Bifidobacterium group, with 10 rats in each group. The Siguan group was given electroacupuncture at the bilateral "Hegu" (LI4) and "Taichong" (LR3), using the disperse-dense wave with a frequency of 2Hz/10Hz for 30 minutes each time. The changes in depressive behaviors of rats were observed according to the sucrose consumption and the scores of the open field test of rats in each group. The gene data of the intestinal flora of rats in each group were extracted to analyze the differences in the diversity, composition structure and function of the intestinal flora among different groups. RESULTS: The scores of the depression behavior indexes of the PSD rats in the Siguan group were higher than those in the PSD group. Meanwhile, there were disorders in the structure and function of the intestinal flora of the PSD rats. Compared with the PSD group, both the Siguan group and the Bifidobacterium group had increased contents of beneficial bacteria (Firmicutes and Clostridia) and decreased contents of pathogenic bacteria (Bacteroidetes and Bacteroidia). Compared with the PSD group, the intestinal flora structures of the Siguan group and the Bifidobacterium group were closer to those of normal rats. The abundance of the "Metabolism of Cofactors and Vitamins" functional pathway of the intestinal flora in the Siguan group was lower than that in the PSD group. CONCLUSION: Electroacupuncture at the "Siguan" acupoints can improve the depression-like behaviors of PSD rats by up-regulating intestinal probiotics, down-regulating pathogenic bacteria, restoring the physiological structure of the intestinal flora and regulating the function of the intestinal flora.