To understand the heat tolerance of Esox lucius across different stages of early development and to elucidate appropriate molecular markers for the improvement of heat tolerance traits, this study used upper thermal tolerance (UTT) as an evaluation index, conducted variance analysis of UTT, compared and analyzed the thermal tolerance of Esox Lucius at different developmental stages, and used genotyping-by-sequencing (GBS) to obtain heat tolerance traits that were related to simplified genome sequencing data sets of two extreme groups. We then evaluated heat resistance using a genome wide association study to explore the SNP markers that are associated with heat tolerance traits in Esox lucius. The corresponding results showed that there were significant differences in heat tolerance at different developmental stages during the early development of Esox lucius (P＜0.01). Heat tolerance was highest at the young stage, followed by the juvenile stage, with the lowest heat tolerance being observed at the larval stage. GWAS analysis, combined with FarmCPU and Blink models, showed that the correlations between the five SNPs and the heat tolerance traits of Esox lucius were highly significant (FDR P-value ＜0.01); these SNPs were located in the introns of clstn2, MAPK14, and VAPA genes, and the untranslated region at the 5ʹ end of the ANKS1B gene. These genes are directly or indirectly associated with stimulus and stress responses. In this study, candidate SNPs and genes associated with high temperature tolerance traits were preliminarily screened in Esox Lucius. These results provide a reference for future studies regarding the physiological and molecular mechanisms of high temperature stress tolerance in Esox Lucius, and therefore provide a scientific basis for the improvement of high temperature tolerance in Esox lucius.