Abnormal functional connectivity (FC) at rest has been identified in clinical depressive disorder. However, very few studies have been conducted to understand the underlying neural substrates of subclinical depression. The newly proposed centrality analysis approach has been increasingly used to explore the large-scale brain network of mental diseases. This study aimed to identify the degree centrality (DC) alteration of the brain network in subclinical depressive subjects. Thirty-seven candidates with subclinical depression and 34 well matched healthy controls (HCs) were recruited from the same sample of college students. All subjects underwent a resting-state fMRI (rs-fMRI) scan to assess the DC of the whole brain. Compared with controls, subclinical depressive subjects displayed decreased DC in the right parahippocampal gyrus (PHG), left PHG/amygdala, and left caudate and elevated DC in the right posterior parietal lobule (PPL), left inferior frontal gyrus (IFG) and left middle frontal gyrus (MFG). In addition, by using receiver operating characteristic (ROC) analysis, we determined that the DC values in the regions with altered FC between the two groups can be used to differentiate subclinical depressive subjects from HCs. We suggest that decreased DC in subcortical and increased DC in cortical regions might be the neural substrates of subclinical depression.