<p>This study aims to investigate potential changes in network controllability and structural-function coupling in cerebral small vessel disease (CSVD). Fifty-one CSVD patients and forty-one elderly controls underwent diffusion tensor imaging and resting-state functional magnetic resonance imaging. Average controllability and modal controllability were calculated using network control theory. Structural connectivity and functional connectivity were constructed respectively. Structural–functional coupling in each region was assessed using Spearman’s rank correlation. Cognitive function was assessed using the Mini-Mental Scale Examination (MMSE) and the Trail Making Test (TMT). CSVD patients showed higher global average controllability but lower average controllability within the left prefrontal cortex. Additionally, they exhibited lower modular controllability at the global scale and within the Sensorimotor Network, while showing higher modular controllability in the left prefrontal cortex. Global average controllability was negatively correlated with MMSE scores and positively correlated with TMT-A and TMT-B scores. Global modal controllability was positively correlated with MMSE scores and negatively correlated with TMT-A and TMT-B scores. Global and regional changes in average controllability and modular controllability were linked to the severity of white matter injury. Moreover, regional structural–functional coupling was positively correlated with TMT-A scores at the global level, left sensorimotor cortex, and temporal cortex. Positive relationships were observed between TMT-B scores and the global and regional structural–functional coupling of several sub-networks. The integration of control theory and structural-function coupling may provide a comprehensive framework for elucidating the complex dynamics of CSVD and its association with cognitive impairment.</p>