Study Objectives: Autonomic impairment and white matter (WM) alterations have been noted as effects of obstructive sleep apnea (OSA). This study sought to evaluate the change of WM integrity in patients with OSA using diffusion tensor imaging (DTI) and to determine its relationship with autonomic impairment. Methods: A total of 30 patients with moderate and severe OSA and 19 healthy volunteers were recruited. A cardiovascular autonomic survey was performed and the baroreflex sensitivity (BRS) for each participant was derived from changes in heart rate and blood pressure during the early part of phase II of the Valsalva maneuver. DTI-related indices were derived from DTI. The fractional anisotropy (FA), mean diffusivity (MD), axial diffusivity (AD), and radial diffusivity (RD) maps were compared using voxel-based statistics to determine differences between the patients with OSA and the healthy controls. The correlations among DTI indices, clinical severity, and autonomic parameters were investigated. Results: The BRS values were significantly worse in the OSA group than in the control patients. An exploratory group-wise comparison between the two groups revealed that the patients with OSA exhibited low FA, increased MD, AD, and RD in several brain locations. The declined DTI indices in autonomic-related areas were significantly correlated with increased clinical disease severity and baroreflex impairment. Conclusions: OSA alters WM integrity in the cingulum and temporal lobe, and this impairment might play some role in autonomic dysfunction. The possible interaction between autonomic dysfunction and central nervous system microstructural alterations may represent variant hypoxic patterns, sympathetic activation, and their consequent processes in OSA.