We explore cerebral reorganization in patients with spinal cord injury (SCI) using structural and functional magnetic resonance imaging (fMRI) to investigate regions relative to the prognosis of sensory-motor ability within SCI patients. Thirty right-handed SCI patients and 30 gender- and age-matched healthy controls (HCs) were included. Gray matter volume (GMV) changes in SCI patients were observed and the amplitude of low-frequency fluctuations (ALFF) values within regions with significant differences in GMV were calculated. These altered gray matter regions were used as regions of interest (ROIs) for functional connectivity (FC) analysis to detect related functional changes. Additionally, the Granger causality analysis (GCA) was used to study alterations in effective connectivity (EC) within the brain. The potential association between all the above MRI values with the International Standards for Neurological Classification of Spinal Cord Injury (ISNCSCI) scores was investigated through partial correlation analysis. SCI patients showed reduced GMV in bilateral putamen compared to the HCs. Meanwhile, significant lower FC were found between the bilateral putamen and the right superior parietal gyrus, whereas significant higher FC were found between the right putamen and the bilateral precuneus in patients with SCI. GCA revealed enhanced EC from the left precuneus to the right putamen. The degree of functional alterations with the putamen might hint at the level of sensory-motor function of patients following SCI. When multisensory integration was decreased due to disease, the increased connection between the precuneus and the putamen might serve a role in SCI recovery by increasing visuospatial integration.