The effect of white matter hyperintensities (WMHs) on 50 major WM tractometries was investigated. Elevated WMHs load on white matter tract was associated with lower apparent fiber density (AFD) on tractometery, showing the co-localization of WMH with AFD change. Reduced AFD is associated with lower connectivity of the WM tract. Differences in these metrics between lower WMH and higher WMH groups, and between lower WMH and MCI groups are significant. Moreover, AFD is lower in individuals with MCI, supporting a role of white matter microstructure in cognitive decline.