Sleep deprivation leads to disturbance of the autonomic nervous system, which plays an important role in maintaining the stability of the cardiovascular system. Heart rate variability (HRV) analysis is a non-invasive and reliable tool in evaluating the activities of cardiovascular autonomic nervous system. In recent years, many studies focused on the evaluation of cardiac autonomic modulation in conditions of normal sleep and sleep deprivation by means of HRV analysis. Both acute and chronic sleep deprivations were proved to evoke dramatic and complex changes in HRV time-domain and frequency-domain indices. The changes of HRV were closely related to risks of cardiac events. The present article reviewed the studies on the fields mentioned above and brought forward an agenda for future research.