Background Reports on mood regulating circuit (MRC) indicated different activities between depressed patients and healthy controls.The functional networks based on MRC have not been described in major depression disorder (MDD).Both the anterior cingulate cortex (ACC) and thalamus are all the key regions of MRC.This study was to investigate the two functional networks related to ACC and thalamus in MDD.Methods Sixteen patients with MDD on first episode which never got any medication and sixteen matched health controls were scanned by 3.0 T functional magnetic resonance imaging (fMRI) during resting-state.The pregenual anterior cingulate cortex (pgACC) was used as seed region to construct the functional network by cortex section.The thalamus was used as seed region to construct the functional network by limbic section.Paired-t tests between-groups were performed for the seed-target correlations based on the individual fisher z-transformed correlation maps by SPM2.Results Depressed subjects exhibited significantly great functional connectivity (FC) between pgACC and the parahippocampus gyrus in one cluster (size 923) including left parahippocampus gyrus (-21,-49,7),left parietal lobe (-3,-46,52) and left frontal lobe (-27,-46,28).The one cluster (size 962) of increased FC on thalamus network overlapped the precuneus near to right parietal lobe (9,-52,46) and right cingulate gyrus (15,-43,43) in health controls.Conclusions Abnormal functional networks exist in earlier manifestation of MDD related to MRC by both cortex and limbic sections.The increased functional connectivity of pgACC and decreased functional connectivity of thalamus is mainly involved in bias mood processing and cognition.