•Combining key regions of the frontal-limbic network as seeds to explore seed-based whole-brain rs-FC could discriminate bipolar depression (BipD) from unipolar depression (UniD).•Both UniD and BipD showed abnormal functional connectivity, mainly involving the frontal and sensorimotor networks.•Compared with UniD, BipD showed more widespread affected functional connectivity patterns, which primarily included the sensorimotor network. The frontal-limbic circuit is hypothesized as sub-serving emotional regulation. We performed whole brain resting-state functional connectivity (rs-FC) analysis by studying the key hubs of frontal-limbic circuit: anterior cingulate cortex (ACC), bilateral insula subregions, bilateral amygdala (Amy) as seeds, separately, to discriminate bipolar depression (BipD) from unipolar depression (UniD). We compared seed-based rs-FC of the frontal-limbic seeds with whole brain among 23 BipD participants; 23 age, gender, and depression severity matched patients with UniD, and 23 healthy controls (HCs). We also used support vector machine learning to study classification based on the rs-FC of ACC, bilateral insula subregions, and bilateral Amy seeds with whole brain. BipD showed increased rs-FC between the left ventral anterior insula (vAI) seed and the left anterior supramarginal gyrus (aSMG) and left postcentral gyrus, as well as increased rs-FC between left amygdala seed and the left aSMG when compared to HCs and UniD. Compared to UniD, BipD was associated with increased rs-FC between right dorsal anterior insula seed and right superior frontal gyrus, as well as increased rs-FC between left posterior insula seed and right precentral gyrus and right thalamus. Combined rs-FC of ACC, bilateral insula subregions and bilateral Amy seeds with the whole brain discriminated BipD from UniD with an accuracy of 91.30%. Rs-FC of the emotional regulation circuit is more widely disturbed in BipD than UniD. Using rs-FC with this circuit may lead to further developments in diagnostic decision-making.