Chronic obstructive pulmonary disease (COPD) affects a large population and is closely associated with cognitive impairment. However, the mechanisms of cognitive impairment in COPD patients have not been unraveled. This study investigated the change in patterns of intrinsic functional hubs using a degree centrality (DC) analysis. The connectivity between these abnormal hubs with the remaining brain was also investigated using functional connectivity (FC). Nineteen stable patients with COPD and 20 normal controls(NC) underwent functional magnetic resonance imaging (MRI) examinations and clinical and neuropsychologic assessments. We measured the voxel-wise DC across the whole brain gray matter and the seed-based FC between these abnormal hubs in the remaining brain matter; the group difference was calculated. A partial correlation analysis was performed to assess the relationship between the abnormal DC and clinical variables in COPD patients. Compared to NC, the patients with COPD exhibited significantly decreased DC in the right lingual gyrus (LG), bilateral supplementary motor area (SMA), and right paracentral lobule (PCL). A further seed-based FC analysis found that COPD patients demonstrated significantly decreased FC between these abnormal hubs in several brain areas, including the left cerebellum anterior lobe, left lingual gyrus, left fusiform gyrus, right insula, right inferior frontal gyrus, limbic lobe, cingulate gyrus, left putamen, lentiform nucleus, right precuneus, and right paracentral lobule. A partial correlation analysis showed that the decreased DC in the right PCL was positively correlated with the FEV1 and FEV1/FVC, and the decreased DC in the SMA was positively correlated with naming and pH in COPD patients. This study demonstrates that there are intrinsic functional hubs and connectivity alterations that may reflect the aberrant information communication in the brain of COPD patients. These findings may help provide new insight for understanding the mechanisms of COPD-related cognitive impairment from whole brain functional connections.