Heat stress (HS) is a major problem of tomato production worldwide, as it reduces fruit setting due to the adverse effects on pollen development and fertility. In this study, we isolated heat-tolerant (HT) mutants providing improved fruit-setting under long-term ambient high temperature by testing over 4000 lines from the Micro-Tom tomato mutant collection. The HT mutants were categorized into two types, namely those that produced parthenocarpic fruit, and those that produced fruit with seeds. Among the HT mutants, HT7 plants produced fruit with seeds, had a higher fruit number and seeded-fruit yield, and the total pollen number and viability were much higher under HS conditions than those of the WT under both control and HS conditions. HT7 also succeeded at fertilization even under HS conditions due to higher pollen viability than the WT. In addition, HS-related genes, such as SIHsfA1b3 and Hsp101, were more highly expressed in HT7 than in WT. These results suggest that HT7 could be a valuable genetic resource for elucidating heat tolerance mechanisms and a breeding material for improving heat-tolerant fruit-setting in tomato.