We aimed to investigate the different brain activation patterns and alterations in somatosensory pathways in complete spinal cord injury (CSCI) and incomplete spinal cord injury (ISCI) patients and to provide a theoretical basis for the rehabilitation of somatosensory function in SCI patients.Fifteen CSCI patients, 15 ISCI patients and 24 healthy controls (HCs) underwent somatosensory stimulation tasks during brain functional magnetic resonance imaging. The brain activation patterns were compared. On the basis of evidence from the underlying somatosensory pathways, several somatosensory-related brain regions were selected as regions of interest (ROIs). Granger causality analysis (GCA)-an effective connectivity (EC) analysis technique-was used to measure the directional functional information flow among the aforementioned ROIs to detect alterations in the somatosensory pathways.Regarding brain activation patterns, compared with the ISCI and HCs groups, the CSCI group presented significant decreases in brain activation intensity in the bilateral insula (INS) and Rolandic operculum (ROL) (cluster-level FDR correction with p < 0.05). GCA-based EC calculations revealed that compared with the ISCI group, the CSCI group presented lower EC from the right thalamus and INS to the right postcentral gyrus (PoCG) (p < 0.001; p = 0.003; separately). Compared with HCs group, decreased ECs from the right ROL to the right PoCG were found in both the CSCI and ISCI groups (p = 0.001; p = 0.006; separately).In conclusion, CSCI and ISCI patients exhibited different brain activations and alterations in somatosensory pathways, laying the theoretical foundation for somatosensory rehabilitation in SCI patients.Copyright © 2025 The Authors. Published by Elsevier Inc. All rights reserved.