Abstract Childhood obesity is associated with alterations in brain structure. Previous studies generally used a single structural index to characterize the relationship between body mass index(BMI) and brain structure, which could not describe the alterations of structural covariance between brain regions. To cover this research gap, this study utilized two independent datasets with brain structure profiles and BMI of 155 school-aged children. Connectome-based predictive modeling(CPM) was used to explore whether children’s BMI is reliably predictable by the novel individualized morphometric similarity network(MSN). We revealed the MSN can predict the BMI in school-age children with good generalizability to unseen dataset. Moreover, these revealed significant brain structure covariant networks can further predict children’s food approach behavior. The positive predictive networks mainly incorporated connections between the frontoparietal network(FPN) and the visual network(VN), between the FPN and the limbic network(LN), between the default mode network(DMN) and the LN. The negative predictive network primarily incorporated connections between the FPN and DMN. These results suggested that the incomplete integration of the high-order brain networks and the decreased dedifferentiation of the high-order networks to the primary reward networks can be considered as a core structural basis of the imbalance between inhibitory control and reward processing in childhood obesity.