The function of sleep in humans has been investigated using simultaneous electroencephalography (EEG) and functional magnetic resonance imaging recordings to provide accurate sleep scores with spatial precision. Recent studies have demonstrated that spontaneous brain oscillations and functional connectivity dissociate during nonrapid eye movement (NREM) sleep; this leads to spontaneous cognitive processes, such as memory consolidation and emotional modulation. However, variations in network connectivity across the sleep stages or between sleep/wake transitions require further elucidation. We observed changes in the connectivity of the sensorimotor and default-mode networks (DMN) mediated by midnight sleep among 18 healthy participants. The results indicated that (1) functional connectivity in both networks showed increasing dissociation as NREM sleep deepened, whereas hyperconnectivity occurred during rapid eye movement (REM) sleep; and (2) compared with connectivity before sleep, the DMN presented a comparable connectivity pattern immediately after awakening, whereas the connectivity of the sensorimotor network remained disrupted. These findings showed that connectivity patterns dissociate and reconnect coherently in both cortical networks during NREM and REM sleep, respectively. After the person awakened, the DMN connectivity was re-established before the sensorimotor reconnection. These dynamic sleep-related dissociations and reconnections between sleep/wake conditions might provide the key to understanding cognitive modulations in sleep. If so, connectivity changes might serve as an alternative indicator beyond the EEG signature to unveil the spontaneous processes that occur during sleep.