The reproductive stage of rice is vulnerable to heat stress, which reduces spikelet fertility and yield. Auxin significantly influences reproductive development, hence the research aimed to enhance spikelet fertility and grain attributes in rice plants by exploring the application efficiency of Indole-3-acetic acid (IAA) and 1-naphthaleneacetic acid (NAA) under heat stress. This study investigated the effects of IAA (10 μmol L−1) and NAA (100 μmol L−1) on spikelet fertility rate in six rice genotypes during the flowering stage. Compared to the heat stress (HS) treatment, the spikelet production rate and grain yield per plant were higher by 61.16%, 37.25%, and 33.07%, and 72.84%, 44.48%, and 32.71% in control, HS + NAA, and HS + IAA treatments, respectively. In addition, panicle weight, primary branches number panicle−1, and 1000-grains weight were significantly (p < 0.05) improved with HS + IAA and HS + NAA application under heat stress conditions. Auxin application enhanced photosynthetic and transpiration rate, while contrarily, leaf temperature diminished. The higher photosynthetic rate showed positive relationships with spikelet fertility (r = 0.64) and yield plant−1 (r = 0.63). Additionally, leaf temperature had a strongly negative correlation (r = −0.81) with the spikelet fertility rate. The application of auxin increased the number of filled grains panicle−1, which showed a positive relationship (r = 0.75) with grain yield plant−1. The variation of spikelet fertility rate among genotypes was dependent on the variety tolerance rate. Overall, these findings indicate that exogenous auxin application can mitigate the negative impact of heat stress on rice and improve spikelet fertility and grain yield.