The rapid shifts of society have brought about changes in human behavioral patterns, with increased evening activities, increased screen time, and postponed sleep schedules. As an explicit manifestation of circadian rhythms, chronotype is closely intertwined with both physical and mental health. Night owls often exhibit more unhealthy lifestyle habits, are more susceptible to mood disorders, and have poorer physical fitness. Although individual differences in chronotype yield varying consequences, their neurobiological underpinnings remain elusive. Here we carry out a pattern-learning analysis, and capitalize on a vast array of ~ 1,000 phenome-wide phenotypes with three brain-imaging modalities (region volume of gray matter, whiter-matter fiber tracts, and functional connectivity) in 27,030 UK Biobank participants. The resulting multi-level depicts of brain images converge on the basal ganglia, limbic system, hippocampus, as well as cerebellum vermis, thus implicating key nodes in habit formation, emotional regulation and reward processing. Complementary by comprehensive investigations of in-deep phenotypic collections, our population study offers evidence of behavioral pattern disparities linked to distinct chronotype-related behavioral tendencies in our societies.