The structure and function of the human brain is closely related to cognitive processes of the mind and physiological processes of the body, suggesting that an intricate relationship exists between cognitive health, body health, and underlying neural architecture. In the current study, morphometric differences in cortical and subcortical gray matter regions, white matter integrity, and resting-state functional connectivity was assessed to determine what combinations of neural variables best explain an interconnected behavioral relationship between body mass index (BMI), general intelligence, and specific measures of executive function. Data for 82 subjects were obtained from the Nathan Kline Institute Rockland Sample. Behavioral results indicated a negative relationship between BMI and intelligence, which exhibited mediation by an inhibitory measure of executive function. Neural analyses further revealed generally contrasting associations of BMI, intelligence, and executive function with cortical morphometric regions important for inhibitory control and directed attention. Moreover, BMI related to morphometric alterations in components of a frontolimbic network, namely reduced thickness in the anterior cingulate cortex and ventromedial prefrontal cortex, whereas intelligence and inhibitory control primarily related to increased thickness and volume in parietal regions, as well as significantly increased across-network connectivity of visual and default mode resting-state networks. These results propose that medial prefrontal structure and interconnected frontolimbic and frontoparietal networks are important to consider in the relationship between BMI, intelligence, and executive function.