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Major depressive disorder (MDD) is one of the most common affective disorders which ranks among the top causes of worldwide disease burden and disability. Recent studies suggested that MDD resulted in the functional connectivity alteration in the resting state brain networks, such as the emotional circuit and the default mode network (DMN). In addition to these emotion-relevant networks, some other brain regions, such as cuneus gyrus, lingual gyrus and precuneus gyrus, were reported that the activity reduced while performing cognitive tasks. In this study, we examined three networks, i.e. the emotional circuit, the default mode network, and the whole brain network, derived from resting-state functional magnetic resonance imaging (fMRI) to investigate the difference between MDD patients and normal subjects. Furthermore, we explored whether there is another network affected by MDD. The functional MRI data was acquired from 22 healthy subjects and 20 patients with MDD. All images of each subject were parcellated into 90 cortical and sub-cortical regions which were defined as the nodes of the network. The functional relations between the 90 regions were estimated by the time-frequency normalized mutual information (TFNMI). We found that the functional connectivity between any pair of brain regions within each of the three networks was significantly decreased in MDD group by using the t test. The significantly decreased connectivity for MDD in emotional circuit was found in the frontal lobe and between the frontal cortex and limbic regions, and that in DMN exhibited between the frontal cortex and superior temporal cortex. However, in the whole brain network, the most significantly decreased connectivity was revealed in occipital lobe, parietal-occipital, and frontal-occipital regions. Our findings suggested that the functional brain network affected by MDD comprised not only the frontal and limbic regions but also the parts of the parietal and occipital lobe.