Objective To explore the effect of deep transcranial magnetic stimulation （dTMS） on spontaneous neural activity of patients with depressive disorder. Methods Seventeen patients with depressive disorder at the Mental Health Center of the First Hospital of Hebei Medical University from September 2022 to January 2024 were selected as research group， and 10 healthy individuals who underwent physical examinations at the Health Examination Center of the First Hospital of Hebei Medical University from September 2021 to August 2023 were selected as control group. Research group underwent the left dorsolateral prefrontal cortex dTMS at a frequency of 18 Hz， with a stimulation intensity of 120% of the resting exercise threshold. The treatment was conducted five times a week for two consecutive weeks， totaling 10 times. General data of the subjects were collected. Hamilton Depression Scale （HAMD） and Hamilton Anxiety Scale （HAMA） were used to evaluate the depressive disorder and anxiety of research group patients before and after treatment， and resting state functional magnetic resonance imaging （rs-fMRI） of the subjects' heads were collected. Fraction amplitude of low-frequency fluctuation （fALFF） was used to evaluate the spontaneous neural activity of the research group patients before and after treatment， as well as the research group patients before treatment and control group. T-test or non-parametric test were used to evaluate the spontaneous neural activity in research group before and after treatment， while Pearson correlation was used to analyze the association between clinical symptoms and spontaneous neural activity. Results Research group included 16 cases， and control group included 10 cases. The total HAMA score， HAMD score， and factor scores of research group after treatment were all lower than before treatment， and the difference was statistically significant （P＜0.05）. The fALFF value of right paracentral lobule in the research group before treatment was lower than that in the control group， and the difference was statistically significant （t=5.36， P ＜ 0.05）. After dTMS treatment， the fALFF values of the left middle frontal gyrus and right medial superior frontal gyrus decreased， while the fALFF values of the right lingual gyrus， left lingual gyrus， right occipital gyrus， and right paracentral lobule increased， with statistically significant differences （t=12.36，16.01，-11.07，-10.81，-10.19， -14.14； P＜ 0.05）. Pearson correlation analysis showed that the fALFF value of the left lingual gyrus before treatment was negatively correlated with the total HAMA score （r=-0.89， P=0.017） and anxiety/somatic factor score （r=-0.96， P=0.002）， while the decrease in fAFLL value of the left frontal gyrus after treatment was positively correlated with the decrease in retardation factor score （r=0.88， P=0.021）， and the differences were statistically significant. Conclusions Abnormal spontaneous neural activity is present in the frontal， lingual， and occipital lobes of patients with depressive disorder. The balance of spontaneous neural activity after dTMS treatment is related to the improvement of depressive， anxious， and delayed symptoms.