The current clinical practice has established guidelines to assess influences of severity of autonomic injury on the control of heart and blood pressure following spinal cord injury (SCI). However, the influences of SCI-induced autonomic impairment on microvascular dysfunction have not yet been established. Heart rate variability (HRV) has been shown to be a potential tool for quantifying residual sympathovagal regulation of the cardiovascular system following SCI and may be used to assess the effect of autonomic injury on skin microvascular dysfunction. A total of 26 people were recruited into the study, including 12 people with SCI and 14 nondisabled controls. HRV and sacral skin intervals and sacral skin perfusion were continually recorded during 10 min upright and 10 min prone postures. The sympathovagal balance was defined as the ratio of the power of the low frequency to the high frequency of HRV. The results showed that postural changes of nondisabled people produced significant changes in the sympathovagal balance; lower sympathovagal balance was associated with higher skin perfusion (p < 0.05). People with SCI did not show a significant change of HRV and skin perfusion in response to postural changes. In this study, we have demonstrated that the sympathovagal balance assessed by HRV was associated with the skin vasoconstrictive response to postural changes.