Antioxidant enzymes and heat shock proteins are important proteins for Agaricus bisporus to resist adversity stress. Under high temperature stress, mycelia can reduce the damage of itself through the differential expression of their genes. In this study, the mycelia of A. bisporus were treated with 40°C heat stress for 0–120min. It was found that with the extension of heat stress duration, the growth rate of mycelia decreased, aerial mycelia increased, and mycelia bifurcated significantly. Transcriptome analysis of the differential expression of antioxidant enzymes and heat shock protein genes indicated that the antioxidant enzyme genes gpx, ppo3 and cat3 and the heat shock protein genes hsp, hsp70-1 and hsp70-17 were significantly up-regulated under heat stress for 30–60 minutes, while the antioxidant enzyme genes ppo1, ppo2 and cat2 and the heat shock protein genes hsp16, hsp70-14, hsp70-3 and hsp70-16 were significantly up-regulated under heat stress for 90–120min. The result of tracking antioxidant enzyme activity showed that heat stress could activate catalase (CAT) and peroxidase (POD), and increase enzyme activity by 2–3 times; at the same time, heat stress could reduce superoxide dismutase (SOD) activity, but had little effect on polyphenol oxidase (PPO). The study also found that heat stress could make A. bisporus accumulate more O2- which could damage the mycelia. Our research shows that A. bisporus mycelium can resist the damage caused by high temperature stress by activating the expression of different antioxidant enzymes and heat shock protein genes during heat stress. Under such circumstances, CAT and POD might play a major role in scavenging oxidative free radicals. Our preliminary research on high temperature tolerance genes of A. bisporus might provide reference for breeding varieties with high temperature tolerance.