The understanding of human consciousness based on brain connectivity is considered important for brain-machine interfacing. In this study, we investigated changes in causal connectivity in electroencephalography data related to conscious and unconscious experiences during non-rapid eye movement sleep after parietal transcranial magnetic stimulation (TMS). A serial awakening paradigm was used to determine whether subjects had had a conscious experience or not. We calculated direct transfer function (DTF) as a measure of effective connectivity in five frequency bands focusing on frontal and parietal-occipital regions. The DTF showed significant differences in frontal-to-parietal flow between reported unconsciousness and consciousness. During the first 100 ms after TMS, the outward links of the parietal region at low frequencies were higher in no conscious experience than in conscious experience. During the next 100 ms, however, the outward links of the frontal region were higher in the conscious experience than the no conscious experience at low frequencies. Changes with causal connectivity over time after TMS indicate that the spatial roles in brain regions associated with consciousness are different. These findings may help clarify the cortical mechanisms related to conscious experience.