Rice production is facing substantial threats from global warming associated with extreme temperatures. Here we report that modifying a heat stress-induced negative regulator, a negative regulator of thermotolerance 1 (NAT1), increases wax deposition and enhances thermotolerance in rice. We demonstrated that the C2H2 family transcription factor NAT1 directly inhibits bHLH110 expression, and bHLH110 directly promotes the expression of wax biosynthetic genes CER1/CER1L under heat stress conditions. In situ hybridization revealed that both NAT1 and bHLH110 are predominantly expressed in epidermal layers. By using gene-editing technology, we successfully mutated NAT1 to eliminate its inhibitory effects on wax biosynthesis and improved thermotolerance without yield penalty under normal temperature conditions. Field trials further confirmed the potential of NAT1-edited rice to increase seed-setting rate and grain yield. Therefore, our findings shed light on the regulatory mechanisms governing wax biosynthesis under heat stress conditions in rice and provide a strategy to enhance heat resilience through the modification of NAT1.