Genome-wide association study of heat stress tolerance in rapeseed/canola was conducted in greenhouse, growth chamber, and in the field. A total of 37,539 SNP markers were used in this study. In the greenhouse and growth chamber study, 5, 8, and 7 QTL were found associated with pollen sterility, sterile/aborted pods, and number of pods on main raceme, which explained 46.3%, 60.5% and 60.6% phenotypic variations, respectively. In the field study, 6, 11, 7, 11 and 7 QTL were identified causing phenotypic variation of 52.2%, 71.8%, 53.2%, 73.5% and 61.0% for plant height, main raceme height, pods on main raceme, pod length, and pod abortion on main raceme, respectively. Three QTL located on chromosome C05 and, five QTL on chromosome A10 and C03 were identified linked to two common traits sterile/aborted pods, and number of pods on main raceme, respectively. Multiple heat tolerant candidate genes were identified surrounding these QTL.