The aim of this study is to identify the difference of temporal variability among major depressive disorder (MDD) patients (with different early antidepressant responses) and healthy controls (HC), and further explore the relationship between pre-treatment temporal variability and early antidepressant response. At baseline, 77 treatment-naïve inpatients with MDD and 42 matched HC received clinical assessments and 3.0 Tesla resting-state functional magnetic resonance imaging scans. After 2 weeks' antidepressant treatment, the patients were subgrouped into responsive depression (RD, n = 40) and non-responding depression (NRD, n = 37) based on the reduction of Hamilton depression rating scale (HAMD). The temporal variability of 90 brain nodes was calculated for further analysis. Compared with the HC group, both the RD and NRD subjects showed greater baseline temporal variability (i.e., greater dynamic) in the left inferior occipital gyrus. Significantly greater temporal variability in the left pallidum was found in the RD group than the NRD and the HC groups, and the higher variability of left pallidum correlated positively with the HAMD reduction. Moreover, the pooled MDD (i.e., RD and NRD) group showed greater baseline temporal variability in the right inferior frontal gyrus, the left inferior occipital gyrus, the bilateral fusiform gyri and the left Heschl gyrus than the HC group. The distinctive pattern of dynamically reorganized networks may provide a crucial scaffold to facilitate early antidepressant response, and the temporal variability may serve as a promising indicator for the personalized therapy of MDD.