Cerebral small vessel disease (CSVD) is a common chronic and progressive disease that can lead to mental and cognitive impairment. Damage to brain structure and function may play an important role in the neuropsychiatric disorders of patients with CSVD. Increasing evidence suggests that functional changes are accompanied by structural changes in corresponding brain regions. Thus, normal structure–function coupling is essential for optimal brain performance, and disrupted structure–function coupling can be found in many neurological and psychiatric disorders. To date, most studies on patients with CSVD have focused on separate structures or functions, including reductions in white matter volume and blood flow, which lead to cognitive dysfunction. However, there are few studies on brain structure–function coupling in patients with CSVD. In recent years, with the rapid development of multilevel (voxel-wise, neurovascular, regional level, and network level) brain structure–functional coupling analysis methods based on multimodal magnetic resonance imaging (MRI), new evidence has been provided to reveal the correlation between brain function and structural abnormalities and cognitive impairment. Therefore, studying brain structure–function coupling has a potential significance in the exploration and elucidation of the neurobiological mechanism of cognitive impairment in patients with CSVD. This article mainly describes the currently popular brain structure–function coupling analysis technology based on multimodal MRI and the important research progress of these coupling technologies on CSVD and cognitive impairment to provide a perspective for the study of the pathogenesis and early diagnosis of CSVD.