Enhanced antioxidant enzymes activity, particularly superoxide dismutase and catalase, along with autophagy process in reproductive organs, can improve the resilience of rapeseed to heat stress, thereby securing crop yield in the face of global warming. Climate change and global warming have increasingly influenced yield and quality of rapeseed (Brassica napus) almost all across the world. The response of reproductive organs to high-temperature stress was studied in two rapeseed varieties, SAFI5 and DH13 with contrasting levels of heat stress tolerance. Pollen germination, viability, and seed set showed a significant reduction in the heat-sensitive variety (DH13). Superoxide quantification revealed higher accumulation in heat-sensitive variety, leading to decreased seed formation and floret fertility most probably due to declined pollen viability and stigma receptivity. Further microscopic analysis of the anther and pistil demonstrated a significant overlay between the damaged areas and the location of O