Obesity, characterized by excessive adiposity, is associated with brain structural abnormalities. Nevertheless, the relationships between altered structural node of default mode network (DMN), body mass index (BMI), general cognitive ability remained unclear in young adults. In this study, we divided a large sample of young adults into three BMI-based groups. We then conducted one-way analyses of variance and post-hoc tests with Bonferroni corrections to investigate abnormal structural brain regions associated with obesity. Furthermore mediation effects models were built to explore whether the structural alterations influenced the relationship between BMI and general cognitive ability. Compared to their lean and overweight counterparts, young adults with obesity exhibited significantly lower general cognitive ability, higher impulsivity traits, and worse sleep quality. Furthermore, compared with lean group, young adults with obesity exhibited altered cortical thickness of both the left temporal pole and right superior parietal lobule, and abnormal cortical surface area (CSA) of the left entorhinal cortex (EC), a hub within DMN. Moreover, CSA of the left EC mediated the relationship between BMI and general cognitive ability. Obesity was linked to altered structural node of DMN, which mediated general cognitive ability in young adults. These findings indicated the negative effect of obesity on DMN and general cognitive ability in young adults.