Major depressive disorder (MDD) is a common psychiatric condition associated with aberrant large-scale distributed brain networks. However, it is unclear how the network dysfunction in MDD patients is characterized by imbalance or derangement of network modular segregation. Fifty-one MDD patients and forty-three matched healthy controls (HC) were recruited in the present study. We analyzed intrinsic brain activity derived from resting-state functional magnetic resonance imaging (R-fMRI) and then examined brain network segregation by computing the participation coefficient (PC). Further intra- and inter-modular connections analysis were preformed to explain atypical PC. Besides, we explored the potential relationship between the above graph theory measures and symptom severity in MDD. Lower modular segregation of the frontal–parietal network (FPN) was found in MDD compared with the HC group. The MDD group exhibited increased inter-module connections between the FPN and cingulo-opercular network (CON), between the FPN and cerebellum (Cere), between the CON and Cere. At the nodal level, the PC of the anterior prefrontal cortex, anterior cingulate cortex, inferior parietal lobule (IPL), and intraparietal sulcus showed larger in MDD. Additionally, the inter-module connections between the FPN and CON and the PC values of the IPL were negatively correlated with depression symptom in the MDD group. These findings might give evidence about abnormal FPN in MDD from the perspective of modular segregation in brain networks.