The human brain controls various cognitive functions via the functional coordination of multiple brain regions in an efficient and robust way. However, the relationship between consciousness state and the control mode of brain networks is poorly explored. Using multi-channel EEG, the present study aimed to characterize the abnormal control architecture of functional brain networks in the patients with disorders of consciousness (DOC). Resting state EEG data were collected from 40 DOC patients with different consciousness levels and 24 healthy subjects. Functional brain networks were constructed in five different EEG frequency bands and the broadband in the source level. Subsequently, a control architecture framework based on the minimum dominating set was applied to investigate the of control mode of functional brain networks for the subjects with different conscious states. Results showed that regardless of the consciousness levels, the functional networks of human brain operate in a distributed and overlapping control architecture different from that of random networks. Compared to the healthy controls, the patients have a higher control cost manifested by more minimum dominating nodes and increased degree of distributed control, especially in the alpha band. The ability to withstand network attack for the control architecture is positive correlated with the consciousness levels. The distributed of control increased correlation levels with Coma Recovery Scale-Revised score and improved separation between unresponsive wakefulness syndrome and minimal consciousness state. These findings may benefit our understanding of consciousness and provide potential biomarkers for the assessment of consciousness levels.