Tourette syndrome (TS) is a childhood-onset neurobehavioral disorder and its pathophysiological mechanism remains elusive. At present, TS-related abnormalities in either structural connectivity (SC) or functional connectivity (FC) have extensively been described, and discrepancies were apparent between the SC and FC studies. However, abnormalities in the SC-FC correlation for early TS children remain poorly understood. In our study, we used probabilistic diffusion tractography and resting-state FC to construct large-scale structural and functional brain networks for 34 drug-naive TS children and 42 healthy children. Graph theoretical approaches were employed to divide the group-averaged FC networks into functional modules. The Pearson correlation between the entries of SC and FC were estimated as SC-FC coupling within whole-brain and each module. Although five common functional modules (including the sensorimotor, default-mode, fronto-parietal, temporo-occipital and subcortical modules) were identified in both groups, we found SC– FC coupling in TS exhibited increased at the whole-brain and functional modular level, especially within sensorimotor and subcortical modules. The increased SC-FC coupling may suggest that TS pathology leads to functional interactions that are more directly related to the underlying SC of the brain and may be indicative of more stringent and less dynamic brain function in TS children. Together, our study demonstrated that altered whole-brain and module-dependent SC-FC couplings may underlie abnormal brain function in TS, and highlighted the potential for using multimodal neuroimaging biomarkers for TS diagnosis as well as understanding the pathophysiologic mechanisms of TS.