Myricetin, a naturally occurring flavonoid abundant in fruits, vegetables, and medicinal plants, is widely recognized for its strong antioxidant, anti-inflammatory, and anti-cancer activities. However, its regulatory effect on cellular signaling pathways activated by Vibrio (V.) vulnificus cytotoxins has not been fully elucidated. In this study, we investigated the cellular mechanism by which myricetin modulates cytotoxic autophagy induced by the V. vulnificus elastase VvpE in human gastrointestinal epithelial HT-29 cells. Treatment with recombinant VvpE (rVvpE) significantly induced autophagy-dependent cell death in HT-29 cells. Notably, myricetin treatment attenuated this effect by suppressing intracellular reactive oxygen species (ROS) accumulation. The reduction of ROS by myricetin inhibited the subsequent activation of c-Src and protein kinase C (PKC), thereby blocking p38 MAPK phosphorylation in rVvpE-exposed cells. Moreover, myricetin abrogated the activation of nuclear factor-kappa B (NF-κB), leading to downregulation of LC3-II and cleaved caspase-3 expression-key markers of autophagic and apoptotic cell death. Collectively, these findings highlight myricetin as a promising antibiotic-free therapeutic candidate capable of modulating host cellular responses to V. vulnificus infection by targeting the ROS-c-Src-PKC-MAPK-NF-κB signaling axis.