The heat shock transcription factors (Hsfs) play critical roles in plant responses to abiotic stresses. However, the mechanism of Hsfs in the regulation of pollen thermotolerance and their specific biological functions and signaling remain unclear. Herein, we demonstrated that HsfA1a played a key role in tomato pollen thermotolerance. hsfA1a mutants reduced, while its overexpression increased pollen themotolerance based on the pollen viability and germination. Analyzing the whole transcriptome by RNA-Seq data, we found that HsfA1a mainly regulated the genes involved in oxidative stress protection, protein homeostasis regulation and protein modification, as well as the response to biological stress in anthers under heat stress. The accumulation of reactive oxygen species in anthers were enhanced in hsfA1a mutants, while were decreased in HsfA1a overexpressing lines. Furthermore, the bounding of HsfA1a to the promoter region of genes involved in redox regulation (Cu/Zn-SOD, GST8 and MDAR1), protein repair (HSP17.6A, HSP70â2, HSP90â2 and HSP101) and degradation (UBP5, UBP18, RPN10a and ATG10) and regulated the expression of these genes in tomato anthers under heat stress. Our findings suggest that HsfA1a maintains pollen thermotolerance and cellular homeostasis by enhancing the antioxidant capacity and protein repair and degradation, ultimately improving pollen viability and fertility.