Objective Magnetic seizure therapy (MST) is an emerging neuromodulation intervention technique that is widely used in the treatment of major depressive disorder (MDD), but its antidepressant mechanism is still unclear. Therefore, exploring the regulatory effect of MST on the brain functional network of MDD patients with different therapeutic effects is of great significance for the study of the antidepressant mechanism of MST treatment.Methods In this study, the resting-state EEG of 18 MDD patients pre- and post-MST was recorded, and the Pearson correlation method was used to construct the brain functional network; the complex network theory was used to compare and analyze the changes in the topology of the brain functional network; according to the rate of change of the HDRS-17 score, it was further distinguished. The network characteristics were performed a secondary comparison between responders and non-responders.Results The brain functional network connectivity, mean node degree, mean clustering coefficient, and mean global efficiency values were significantly higher than that pre-MST treatment. Mean path length values were significantly lower, and small world attribute significantly increased post-MST treatment. Compared with the group of non-responders, the changes in the characteristic parameters of the brain functional network in the group of responders were significantly larger.Conclusion MST significantly changes the topology of the brain functional network in patients with MDD, and it has a certain modulation effect on the brain functional network of patients. These results provide experimental support and a theoretical basis for the study of the antidepressant mechanism of MST treatment.