Background This study aimed to investigate the alterations in structural integrity of superior longitudinal fasciculus subcomponents with increasing white matter hyperintensity severity as well as the relationship to cognitive performance in cerebral small vessel disease. Methods 110 cerebral small vessel disease study participants with white matter hyperintensities were recruited. According to Fazekas grade scale, white matter hyperintensities of each subject were graded. All subjects were divided into two groups. The probabilistic fiber tracking method was used for analyzing microstructure characteristics of superior longitudinal fasciculus subcomponents. Results Probabilistic fiber tracking results showed that mean diffusion, radial diffusion, and axial diffusion values of the left arcuate fasciculus as well as the mean diffusion value of the right arcuate fasciculus and left superior longitudinal fasciculus III in high white matter hyperintensities rating group were significantly higher than those in low white matter hyperintensities rating group (p < 0.05). The mean diffusion value of the left superior longitudinal fasciculus III was negatively related to the Montreal Cognitive Assessment score of study participants (p < 0.05). Conclusions The structural integrity injury of bilateral arcuate fasciculus and left superior longitudinal fasciculus III is more severe with the aggravation of white matter hyperintensities. The structural integrity injury of the left superior longitudinal fasciculus III correlates to cognitive impairment in cerebral small vessel disease.