Background: Studies have shown that loss of sensorimotor function in spinal cord injury (SCI) leads to brain functional reorganization, which may play important roles in motor function recovery. However, the specific functional changes following SCI are still poorly understood. Purpose: To investigate whether there are functional reorganizations outside the sensorimotor regions after complete thoracolumbar SCI (CTSCI), and how these reorganizations are associated with clinical manifestations. Study Type: Prospective. Subjects: Eighteen CTSCI patients (28-67 years of age; 16 men) and 18 age-, gender-matched healthy controls (HCs) (2764 years of age; 16 men). Field Strength/Sequence: Resting-state functional magnetic resonance imaging (RS-fMRI) using echo-planar-imaging (EPI) sequence at 3.0 T. Assessment: Data preprocessing was performed using Data Processing Assistant for Resting-State fMRI (DPARSF). Amplitude of low-frequency fluctuations (ALFF) was used to characterize regional neural function, and seed-based functional connectivity (FC) was used to evaluate the functional integration of the brain network. Statistical Tests: Two-sample t-tests were used for ALFF and FC measures (the data conform to the normal distribution), partial correlation analysis was used to analyze the correlation between clinical and imaging indicators, and receiver operating characteristic (ROC) analysis was used to search for sensitive imaging indicators. Results: Compared with HCs, CTSCI patients showed decreased ALFF in right lingual gyrus (LG), increased ALFF in right middle frontal gyrus (MFG), and decreased FC between the right LG and Vermis_3 (cluster-level FWE correction with P < 0.05). Subsequent correlation analyses revealed that decreased FC between the right LG and Vermis_3 positively correlated with the visual analog scale (VAS) (P = 0.043, r = 0.443). Finally, the ROC analysis showed that the area under the curve (AUC) of FC value between right LG and Vermis3 was 0.881. Data Conclusion: These findings suggest a possible theoretical basis of the mechanism of visual-, emotion-, and cognition-related techniques in rehabilitation training for CTSCI.