Misdiagnosis of bipolar disorder (BD) as unipolar depression (UD) may cause improper treatment strategy to be chosen, especially in the early stages of disease. The aim of this study was to characterize alterations in specific brain networks for depressed patients who transformed into BD (tBD) from UD.The module allegiance (MA) from resting-fMRI by applying a multilayer modular method was estimated in 99 patients (33 tBD, 33 BD, 33 UD) and 33 healthy controls (HC). A classification model was trained on tBD and UD patients. HC was used to explore the functional declination patterns of BD, tBD and UD.Based on our classification model, difference mainly reflected in default-mode network (DMN). Compared with HC, both BD and tBD focused on the difference of somatomotor network (SMN), while UD on the abnormity of DMN. The patterns of brain network between patients with BD and tBD were well overlapped, except for cognitive control network (CCN).The functional declination of internal interaction in DMN was suggested to be useful for the identification of BD from UD in the early stage. The higher recruitment of DMN may predispose patients to depressive states, while higher recruitment of SMN makes them more sensitive to external stimuli and prone to mania. Furthermore, CCN may be a critical network for identifying different stages of BD, suggesting that the onset of mania in depressed patients is accompanied by CCN related cognitive impairments. This article is protected by copyright. All rights reserved.