The large yellow croaker (Larimichthys crocea ), an economically important marine fish species in China, faces significant challenges due to rising water temperatures caused by global warming. To systematically elucidate the mechanisms underlying high-temperature adaptation and establish a reliable evaluation system for thermal tolerance, this study employed a multi-omics approach, integrating transcriptomic and methylomic sequencing to compare the molecular responses of heat-sensitive and heat-tolerant populations under acute and chronic thermal stress. The results revealed distinct epigenetic regulatory networks and gene expression profiles under different stress conditions, involving coordinated regulation of multiple functional modules, including heat shock proteins, antioxidant systems, and energy metabolism pathways. Given the complexity of the regulatory networks identified through multi-omics analysis, this study innovatively shifted its focus to aerobic metabolism as a core physiological process. By monitoring key physiological indicators such as cardiac function and respiration rates, a systematic and comprehensive assessment of thermal tolerance traits was conducted. The findings not only elucidate the molecular basis of high-temperature adaptation in L. crocea but also provide an aerobic metabolism-centered phenotypic index system for evaluating thermal tolerance. Additionally, this study provides insights for climate-resilient breeding, contributing to the sustainable development of aquaculture under global warming.