Fish oil (FO) is being progressively replaced by palm oil (PO), which is rich in palmitic acid (PA). However, our understanding of the effects of PA on fish and the underlying molecular mechanisms remains limited. Heat shock transcription factor 1 (HSF1) is a critical transcription factor involved in stress response, but whether it responds to the effects of PA in fish remains unknown. In this study, in vitro and in vivo experiments were combined to investigate the molecular mechanisms by which HSF1 responds to PA. Our results indicated that PA induced fat accumulation, inflammation, and activation of protein processing in the endoplasmic reticulum (PPER) in the PaL cells. Moreover, the nuclear translocation of HSF1 was significantly increased by PA. After HSF1 was disrupted using small molecules (HSF1A and KRIBB11) or through HSF1A knockout, the PA-induced fat accumulation and expression levels of key genes related to PPER, lipid metabolism, and inflammation were significantly altered. Additionally, the analysis of CUT&Tag sequencing and dual-luciferase reporter showed that HSF1 protein can directly bind to the promoters of genes involved in PPER, lipid metabolism, and inflammatory response, thereby activating their transcriptional activity, especially HSC70, HSP90α, and HSP90β. Eicosapentaenoic acid (EPA) supplementation significantly improved the survival rate and growth performance of juvenile silver pomfret and reduced PA-induced adverse effects by inhibiting the activation of HSF1 in the liver. This study proves that HSF1 protein may respond to PA-induced lipid metabolism disorder and inflammatory response by maintaining endoplasmic reticulum stability in fish. Furthermore, EPA supplementation effectively counteracts PA-induced adverse effects.