A late chronotype is associated with poor sleep quality, but the fundamental neural mechanism underlying this association remains unclear. Eyes-open resting-state functional MRI scans were obtained from 87 participants after extended wakefulness, and four subregions of the default mode network were extracted and analysed. Partial correlation analysis revealed that the functional connectivity between the precuneus and the medial prefrontal cortex (mPFC) was significantly correlated both with sleep quality and circadian preference of the participants. Mediation analysis found that the precuneus-mPFC link fully mediated the correlation between chronotype and sleep quality. We concluded that increased neural communication in the midline cores of the default mode network (DMN) may be responsible for the poor sleep quality of late chronotypes. As late chronotypes exhibit vulnerability to many mental disorders, our results can be used to refine pathophysiological models and provide therapy for such psychological disorders.