Sleep inertia refers to a distinct physiological state of waking up from sleep accompanied by performance impairments and sleepiness. The neural substrates of sleep inertia are unknown, but growing evidence suggests that this inertia state maintains certain sleep features. To investigate the neurophysiological mechanisms of sleep inertia, a comparison of pre‐sleep and post‐sleep wakefulness with eyes‐open resting‐state was performed using simultaneous EEG‐fMRI, which has the potential to reveal the dynamic details of neuroelectric and hemodynamic responses with high temporal resolution. Our data suggested sleep‐like features of slow EEG power and decreased BOLD activity were persistent during sleep inertia. In the pre‐sleep phase, participants with stronger EEG vigilance showed stronger activity in the fronto‐parietal network (FPN), but this phenomenon disappeared during sleep inertia. A time course analysis confirmed a decreased correlation between EEG vigilance and the FPN activity during sleep inertia. This simultaneous EEG‐fMRI study advanced our understanding of sleep inertia and revealed the importance of the FPN in maintaining awareness. This is the first study to reveal the dynamic brain network changes from multi‐modalities perspective during sleep inertia.