Early life stress (ELS) significantly increases susceptibility to alcohol use disorder (AUD) by affecting the interplay between executive and salience networks (SN). The link between AUD and higher body-mass index (BMI) is known, but we lack understanding of how BMI impacts the relationship between ELS and brain connectivity in individuals with AUD. To bridge this gap, we investigated the effects of ELS on brain connectivity in AUD participants, taking into account differences in BMI. The cohort included 401 individuals with AUD, with approximately 60% having a BMI ≥ 25. Within the overall cohort, 123 participants underwent resting-state functional magnetic resonance imaging, revealing intriguing anticorrelations between SN seeds and brain regions involved in somatosensory processing, motor coordination, and executive control as an effect of ELS. Examining the relationship between ELS-driven brain connectivity and BMI, we observed negative correlations in connectivity among low BMI (≤ 24.9) vs. high BMI (≥ 25) individuals. For example, the left supramarginal gyrus (SMG) seed exhibited decreased connectivity with emotion regulation and decision-making regions, including the right occipital cortex, posterior cingulate cortex, and precuneus clusters (all |β| < -0.03, |p| < 0.05). Additionally, the right SMG seed showed reduced connectivity with impulse control and executive function regions, such as the left postcentral/middle frontal gyrus cluster (β = 0.04, p = 0.02). These findings highlight the role of ELS-induced alterations in SN seed connectivity, influenced by BMI, in the neurobiology of AUD. Understanding the neural mechanisms linking obesity, AUD, and ELS can guide targeted interventions for this population.