Human brain shows higher individual variability in functional connectivity in heteromodal association cortex but lower in unimodal cortex. Structural connectivity is the anatomical substrate of the functional connectivity. However, the spatial pattern of individual variability in structural connectivity still remains unclear. In the present study, we depicted the temporal-spatial pattern of individual variability in structural connectivity, which increases with aging and is lowest in unimodal sensorimotor regions, intermediate in association regions and highest in para-limbic regions. Our results demonstrated that this specific spatial distribution relates to the plasticity of synapse and white matter. Considering the brain systems and pathways involved in a cognition maybe different among individuals, we proposed a modified ridge regression model that is able to predict individual cognition and generate idiographic brain mapping. The individual variability in structural connectivity and idiographic brain mapping is significantly correlated. Overall, our study has potential implications for understanding biological and genetic mechanisms of individual differences in structural connectivity, guiding interventions to promote successful cognitive and interpreting statistical maps in human connectome.