BackgroundPollen tube elongation in the pistil is a key step for pollination success in plants, and auxins play an important role in this process. However, the function of auxins in pollen tube elongation in the pistil of rice under heat stress has seldom been previously reported.ResultsTwo rice genotypes differing in heat tolerance were subjected to heat stress of 40 °C for 2 h after flowering. A sharp decrease in spikelet fertility was found in the Nipponbare (NPB) and its mutant High temperature susceptible (HTS) under heat stress, but the stress-induced spikelet sterility was reversed by 1-naphthaleneacetic acid (NAA), especially the HTS. Under heat stress, the pollen tubes of NPB were visible in ovule, while those of HTS were invisible. However, we found the pollen tubes in ovule when sprayed with NAA. During this process, a significant increase in indole-3-acetic acid (IAA) and reactive oxygen species (ROS) levels was found in the pistil of heat-stressed NPB, while in heat-stressed HTS they were obviously decreased. Additionally, the peroxidase (POD) activity in pistil of NPB was significantly decreased by heat stress, whereas there was no difference between the heat-stressed and non-heat-stressed pistils of HTS.ConclusionIt was concluded that the enhancement of heat tolerance in plants by NAA was achieved through the increase of the levels of auxins, which prevented the inhibition of pollen tube elongation in pistil, and the crosstalk between auxins and ROS, which might be involved in this process. In addition, POD might be a negative mediator in pollen tube elongation under heat stress due to its ability to scavenge ROS and degrade auxin.Electronic supplementary materialThe online version of this article (10.1186/s12284-018-0206-5) contains supplementary material, which is available to authorized users.