The reproductive stage of rice is the most sensitive to heat stress, which can lead to spikelet sterility. Thus, heat-tolerant and heat-susceptible genotypes were used to investigate their differences in terms of phenotypic responses and expression changes of Hsf genes at the pre-flowering stage under heat stress. Results clearly showed that panicles had the highest temperature compared with other plant parts under both natural and heated conditions. However, the temperatures of tolerant and susceptible genotypes were not significantly different. In terms of spikelet fertility, the tolerant lines M9962 and M7988 had high seed set because their anther dehiscence, pollen viability and pollen germination were only slightly affected. In contrast, the susceptible line Sinlek showed severe effects at all steps of fertilization, and the pollen viability of M7766 was slightly affected under heat stress but was more affected in terms of anther dehiscence and pollen germination. Both susceptible lines showed dramatically decreased seed set. In addition, the expression of six HsfA genes in the flag leaves and spikelets at the R2 stage of plants under heat stress showed different responses. Notably, expression of the HsfA2a gene was predominantly upregulated in the flag leaf and spikelets under heat stress in M9962. Therefore, it can be concluded that heat stress has severe effects on the stamen, and that different genotypes have different susceptibilities to heat stress.