Chronotype is an inherent physiological trait reflecting an individual's subjective preference for their sleep awakening time, exerting a substantial influence on both physical and mental well-being. While existing research has established a close relationship between chronotype and individual brain structure, prior studies have predominantly focused on individual measurements of brain structural scales, thereby limiting the exploration of the underlying mechanisms of structural changes. This study seeks to validate previous research findings and enhance our understanding of the correlation between circadian rhythm preference and diverse cortical indicators in healthy young individuals. Magnetic resonance imaging (MRI) scans and chronotype assessments were conducted once for all participants, comprising 49 late chronotype (LC) young adults and 49 matched early chronotype young adults. The Chronotype Questionnaire was utilized to assess morningness and eveningness preferences. Surface-based analysis of structural MRI data revealed that LC young adults exhibited thinner cortical thickness of left pars orbitalis and lower cortical mean curve of right paracentral gyrus. Overall, this study represents a significant advancement in elucidating the connection between brain structure and function within the context of chronotypes.