Heat shock factors (HSFs) play a crucial role in the environmental stress responses of numerous plant species, including defense responses to pathogens; however, their role in cotton resistance to remains unclear. We have previously identified several differentially expressed genes (DEGs) in after inoculation with . Here, we discovered that in (cotton) after inoculation with shares a high identity with a DEG in in response to infection. Quantitative real-time PCR (qRT-PCR) analysis indicated that expression was rapidly induced by and ubiquitous in cotton roots, stems, and leaves. In a localization analysis using transient expression, GhHSFA4a was shown to be localized to the nucleus. Virus-induced gene silencing (VIGS) revealed that downregulation of significantly increased cotton susceptibility to To investigate mediated defense, 814 DEGs were identified between silenced plants and controls using comparative RNA-seq analysis. The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that DEGs were enriched in "flavonoid biosynthesis", "sesquiterpenoid and triterpenoid biosynthesis", "linoleic acid metabolism" and "alpha-linolenic acid metabolism". The expression levels of marker genes for these four pathways were triggered after inoculation with . Moreover, -overexpressing lines of displayed enhanced resistance against compared to that of the wild type. These results indicate that is involved in the synthesis of secondary metabolites and signal transduction, which are indispensable for innate immunity against in cotton.