Deep medullary vein (DMV) hypo-visibility is correlated with white matter hyperintensity (WMH), but the underlying causes remain unclear. This study aimed to explore the relationship between deep vein diameters and perivascular space (PVS) scores, and DMV hypo-visibility in the presence of WMH. This cross-sectional study prospectively analyzed the clinical and imaging data of 190 cerebral small vessel disease patients with WMH and 40 healthy controls from the Lishui Hospital of Traditional Chinese Medicine affiliated with Zhejiang Chinese Medical University. PVS scores ranging from 0 to 4 were determined according to the PVS counts in the basal ganglia area on T2-weighted magnetic resonance images; high-grade PVS was defined as a PVS score >1. The diameters of the deep cerebral veins, including the bilateral septal veins (SVs), thalamostriate veins (TSVs), lateral ventricular veins (LVVs), and internal cerebral veins, were measured using susceptibility weighted imaging (SWI). Left and right DMV scores, ranging from 0 to 9, were calculated based on the visibility of the DMV on SWI in the ipsilateral frontal, parietal, and occipital lobes. The deep cerebral vein diameters, left and right DMV scores, and high-grade PVS differed between the healthy controls and WMH patients (P<0.05). Left DMV scores were independently associated with age {β [95% confidence interval (CI)]: 0.050 (0.018, 0.082)}, high-grade PVS [β (95% CI): 0.998 (0.262, 1.737)], and the diameters of the ipsilateral SVs [β (95% CI): -1.114 (-1.754, -0.475)], SVs [β (95% CI): -0.734 (-1.191, -0.277)], and LVVs [β (95% CI): -0.921 (-1.567, -0.275)] [all false discovery rate (FDR)-corrected P<0.05]. Right DMV scores were independently associated with age [β (95% CI): 0.071 (0.037, 0.105)], high-grade PVS [β (95% CI): 0.873 (0.111, 1.635)], and the diameters of the ipsilateral SVs [β (95% CI): -0.837 (-1.386, -0.289)], TSVs [β (95% CI): -0.875 (-1.331, -0.419)], and LVVs [β (95% CI): -1.813 (-2.484, -1.142)] (all FDR-corrected P<0.05). Decreased hypo-visibility of DMVs on SWI was associated with a higher age, the presence of high-grade PVS, and smaller diameters of the ipsilateral deep cerebral veins in individuals with WMH. Our findings provide novel insights into the probable mechanisms leading to high DMV scores.