Traumatic complete spinal cord injury (CSCI) leads to severe impairment of sensory-motor function, and patients often suffer from neuropsychological deficits such as anxiety, depression, and cognitive deficits, which involve different brain functional modules. However, the alterations in modular organization and the interactions between these modules in pediatric patients with CSCI remain unclear. In this study, a total of 70 participants, including 34 pediatric CSCI patients and 36 healthy controls (HCs) aged 6 to 12 years, underwent whole-brain resting-state functional MRI. The functional networks were analyzed via a graph theory approach based on the 90-region Automated Anatomical Labeling (AAL 90) atlas, generating a 90 x 90 correlation matrix. Metrics for nodal, global, and modular scales were calculated to evaluate alterations in the network's topology. Between-group comparisons and partial correlation analysis were performed. Compared to HCs, pediatric CSCI patients exhibited significant decreases in nodal metrics, particularly in subcortical networks (SN) like the bilateral thalamus. Besides, the distribution of core nodes changed, with five newly added core nodes primarily located in the regions of the default mode network (DMN). For modular interactions, patients group presented increased connectivity within the DMN and between the DMN and the attention network (AN) but reduced connectivity between DMN and SN, DMN and vision network (VN), and AN and SN. Notably, the participation coefficient (Pc) of the TPOmid.L (left temporal pole: middle temporal gyrus) was positively correlated with motor scores, suggesting its potential as an indicator for evaluating the motor function in pediatric CSCI patients. Additionally, the patients demonstrated a different modular structure with significantly lower modularity. These findings suggest that functional network and modular alterations chiefly occur in emotional cognition and vision-associated regions, emphasizing the importance to focus on their psychocognitive well-being and providing evidence for visual-feedback related rehabilitation strategies.