This study aimed to assess the relationship between breakfast composition and long-term regular breakfast consumption and cognitive function. Participants included 835 children from the China Jintan Cohort Study for the cross-sectional study and 511 children for the longitudinal study. Breakfast consumption was assessed at ages 6 and 12 through parental and self-administered questionnaires. Cognitive ability was measured as a composition of IQ at age 6 and 12 and academic achievement at age 12, which were assessed by the Chinese versions of the Wechsler Intelligence Scales and standardized school reports, respectively. Multivariable general linear and mixed models were used to evaluate the relationships between breakfast consumption, breakfast composition and cognitive performance. In the longitudinal analyses, 94.7% of participants consumed breakfast ≥ 4 days per week. Controlling for nine covariates, multivariate mixed models reported that compared to infrequent breakfast consumption, regular breakfast intake was associated with an increase of 5.54 points for verbal and 4.35 points for full IQ scores (p < 0.05). In our cross-sectional analyses at age 12, consuming grain/rice or meat/egg 6–7 days per week was significantly associated with higher verbal, performance, and full-scale IQs, by 3.56, 3.69, and 4.56 points, respectively (p < 0.05), compared with consuming grain/rice 0–2 days per week. Regular meat/egg consumption appeared to facilitate academic achievement (mean difference = 0.232, p = 0.043). No association was found between fruit/vegetable and dairy consumption and cognitive ability. In this 6-year longitudinal study, regular breakfast habits are associated with higher IQ. Frequent grain/rice and meat/egg consumption during breakfast may be linked with improved cognitive function in youth.