Background: The mechanism by which antidepressants normalizing aberrant resting-state functional connectivity (rsFC) in patients with major depressive disorder (MDD) is still a matter of debate. The current study aimed to investigate aberrant rsFC and whether antidepressants would restore the aberrant rsFC in patients with MDD. Methods: A total of 196 patients with MDD and 143 healthy controls (HCs) received the resting-state functional magnetic resonance imaging and clinical assessments at baseline. Patients with MDD received antidepressant treatment after baseline assessment and were re-scanned at the 6-month follow-up. Network-based statistics were employed to identify aberrant rsFC and rsFC changes in patients with MDD and to compare the rsFC differences between remitters and non-remitters. Results: We identified a significantly decreased sub-network and a significantly increased sub-network in MDD at baseline. Approximately half of the aberrant rsFC remained significantly different from HCs after 6-month treatment. Significant overlaps were found between baseline reduced sub-network and follow-up increased sub-network, and between baseline increased sub-network and follow-up decreased sub-network. Besides, rsFC at baseline and rsFC changes between baseline and follow-up in remitters were not different from non-remitters. Conclusions: Most aberrant rsFC in patients with MDD showed state-independence. Although antidepressants may modulate aberrant rsFC, they may not specifically target these aberrations to achieve therapeutic effects, with only a few having been directly linked to treatment efficacy.