Sleep is indispensable for humans to maintain normal life activities. Sex and individual differences in sleep patterns and quality of sleep cannot be ignored. Nevertheless, the overall population generalities and sex-or individual-differences in cerebral cortical functional connectivity (FC) during sleep have not been well described. Here, we evaluated the characteristic patterns of FC based on whole-night sleep electroencephalography (EEG) recordings. An improved weighted phase lag index (WPLI) algorithm was applied to obtain the FC in delta (0.5-4Hz), theta (4-8Hz), alpha (8-12Hz) and beta band (12-32Hz). FC strength, short-term stability and inter-regional imbalance of FC were studied. We found that the variations in FC-related parameters among sleep stages had overall population commonalities, and these parameters also showed stage-and frequency band-dependent sex differences. With the deepening of norapid eye movement (NREM), increased delta and beta FC strength were observed. Rapid eye movement (REM) showed weaker FC strength, higher FC stability, and higher anterior-posterior FC anisotropy than NREM in beta band. Meanwhile, females exhibited higher sleep EEG synchronization and higher delta FC stability in deep NREM sleep than males. Moreover, the dominant hemisphere in terms of FC did not show group generality or stage-and frequency-dependence. Our results add to the understanding of sleep staging function and may provide clues to sex differences in sleep patterns and quality as well as the prevalence and clinical manifestations of sleep-related illness. Short-term stability offers a new perspective in analyzing FC, which cannot be ignored.INDEX TERMS Overall population generalities, sex differences, sleep stages, sleep EEG, functional connectivity.