Objective To explore the neurobiological mechanism and the underlying effect of repetitive transcranial magnetic stimulation （rTMS） treatment in patients with first-episode major depression disorder （MDD）， using the amplitude of low-frequency fluctuation （ALFF） of resting-state functional magnetic resonance imaging （fMRI）. Methods A total of 35 patients with first-episode MDD treated in the Department of Psychiatry of the First Affiliated Hospital of Air Force Medical University from May 2019 to December 2020 were recruited as the treatment group. Another 37 healthy individuals matched in gender， age and education with the treatment group were recruited through advertisements as the control group. Resting fMRI scans were performed in both groups. The treatment group underwent fMRI scan again after 15 days of rTMS treatment， and at the same time the two groups were evaluated by clinical scale. The fMRI data was processed by DPABI software， and the ALFF value of the whole brain of the two groups of subjects was calculated and compared and analyzed. Results The scores of the Hamilton Depression Scale （HAMD-17） ［22.00 （20.25， 24.00）vs 10.00 （8.00， 11.75）， U=40.50， P＜0.001］， Generalized Anxiety Scale （GAD-7） ［8.50 （6.00， 11.00） vs 6.00 （4.25， 7.00）， U=234.00， P＜ 0.001］ and Patient Health Questionnaire （PHQ-9） ［14.50 （12.00， 19.00） vs 9.00 （6.00， 11.75）， U=138.50， P＜ 0.001］ of the treatment group decreased significantly after rTMS treatment， and the differences were statistically significant （P ＜ 0.001）. After the treatment， the MDD patients showed increased ALFF in the right superior frontal gyrus ［-1.02 （-1.08， -0.67） vs -0.68 （-0.99， -0.29）， U=217.00， P=0.007］ and right inferior temporal gyrus ［-0.50 （-0.67， -0.33） vs -0.29 （-0.41， -0.08）， U=173.00， P ＜ 0.01］， while decreased ALFF in the right superior marginal gyrus ［0.89 （0.46， 1.13） vs 0.36 （0.06， 0.81）， U=228.00， P=0.012］ and left posterior cingulate gyrus ［1.09 （0.81， 1.39） vs 0.69 （0.05， 1.00）， U=198.00， P=0.002］. The post-comparison results of ANOVA analysis showed that the differences of ALFF values between after rTMS treatment in MDD patients and health controls were not statistically significant （P＞ 0.05）， suggesting that these brain areas tended to be normal or reversed after rTMS treatment. Conclusions rTMS treatment can enhance the activity intensity of the superior frontal gyrus and inferior temporal gyrus and reduce the activity intensity of the superior marginal gyrus and posterior cingulate gyrus， thus playing dynamic balance regulation effect on the brain function of patients with MDD.