ABSTRACT Preserving a normal body mass index (BMI) is crucial for the healthy growth and development of children. As a core aspect of executive functions, inhibitory control plays a pivotal role in maintaining a normal BMI, which is key to preventing issues of childhood obesity. By studying individual variations in inhibitory control performance and its associated connectivity-based neuromarker in a sample of primary school students (N = 64; 9–12 yr), we aimed to unravel the pathway through which inhibitory control impacts children’s BMI. Utilizing resting-state functional MRI scans and a connectivity-based psychometric prediction framework, we found that enhanced inhibitory control abilities were primarily associated with increased functional connectivity in brain structures vital to executive functions, such as the superior frontal lobule, superior parietal lobule, and posterior cingulate cortex. Conversely, inhibitory control abilities displayed a negative relationship with functional connectivity originating from reward-related brain structures, such as the orbital frontal and ventral medial prefrontal lobes. Furthermore, we revealed that both inhibitory control and its corresponding neuromarker can moderate the association between food-related delayed gratification and BMI in children. However, only the neuromarker of inhibitory control maintained its moderating effect on children’s future BMI, as determined in the follow-up after one year. Overall, our findings shed light on the potential mechanisms of how inhibitory control in children impacts BMI, highlighting the utility of the connectivity-based neuromarker of inhibitory control in the context of childhood obesity.