In this study, we observed miRNA and mRNA transcriptomic changes in multiple reward-related or alcohol-responsive brain regions of AUD subjects. We also discovered that brain region-specific miRNA–mRNA interactions potentially contribute to biological pathways important for AUD risk. Through the in vitro cellular model study, we validated that alcohol exposure could alter miRNA and mRNA expression profiles and miRNA–mRNA regulatory networks. To our knowledge, this is the first study that investigated the relationship of AUD and brain miRNA–mRNA regulatory networks.