Background: Brain imaging results in sleep deprived patients showed structural changes in the cerebral cortex; however, the reasons for this phenomenon need to be further explored. Methods: This MR study evaluated causal associations between morningness, ease of getting up, insomnia, long sleep, short sleep, and the cortex structure. Results: At the functional level, morningness increased the surface area (SA) of cuneus with global weighted (beta(b) (95% CI): 32.63 (10.35, 54.90), p = 0.004). Short sleep increased SA of the lateral occipital with global weighted (b (95% CI): 394.37(107.89, 680.85), p = 0.007. Short sleep reduced cortical thickness (TH) of paracentral with global weighted (OR (95% CI): −0.11 (−0.19, −0.03), p = 0.006). Short sleep reduced TH of parahippocampal with global weighted (b (95% CI): −0.25 (−0.42, −0.07), p = 0.006). No pleiotropy was detected. However, none of the Bonferroni-corrected p values of the causal relationship between cortical structure and the five types of sleep traits met the threshold. Conclusions: Our results potentially show evidence of a higher risk association between neuropsychiatric disorders and not only paracentral and parahippocampal brain areas atrophy, but also an increase in the middle temporal zone. Our findings shed light on the associations of cortical structure with the occurrence of five types of sleep traits.