Compared to healthy controls, spinal cord injury (SCI) patients demonstrate white matter (WM) abnormalities in the brain. However, little progress has been made in comparing cerebral WM differences between SCI-subgroups. The purpose of this study was to investigate WM microstructure differences between paraplegia and quadriplegia using tract-based spatial statistics (TBSS) and atlas-based analysis methods. Twenty-two SCI patients (11 cervical SCI and 11 thoracic SCI) and 22 age- and sex-matched healthy controls were included in this study. TBSS and atlas-based analyses were performed between SCI and control groups and between SCI-subgroups using multiple diffusion metrics, including fractional anisotropy (FA), mean diffusivity (MD), axial diffusivity (AD) and radial diffusivity (RD). Compared to controls, SCI patients had decreased FA and increased MD and RD in the corpus callosum (CC; genu and splenium), superior longitudinal fasciculus (SLF), corona radiata (CR), posterior thalamic radiation (PTR), right cingulum (cingulate gyrus; CCG) and right superior fronto-occipital fasciculus (SFOF). Cervical SCI patients had lower FA and higher RD in the left PTR than thoracic SCI patients. Time since injury had a negative correlation with FA within the right SFOF (r = -0.452, p = 0.046) and a positive association between the FA of left PTR and the American Spinal Injury Association (ASIA) sensory score (r = 0.428, p = 0.047). In conclusion, our study suggests that multiple cerebral WM tracts are damaged in SCI patients, and WM disruption in cervical SCI is worse than thoracic injury level, especially in the PTR region.