High temperature influence flower bud differentiation in Physalis grisea, resulting in the production of deformed fruits and affects fruit yield and quality. However, the molecular mechanisms underlying the response of P. grisea to heat stress (HS) remain unclear. In this study, HS treatment and dynamic transcriptome analysis of P. grisea identified the PgCDF2-PgHSFA1/PgHSFB3 transcriptional regulatory module as playing a key role in the response of P. grisea to HS. Gene Ontology (GO) enrichment analysis, transcriptional regulation prediction, and weighted correlation network analysis (WGCNA) of heat stress (HS)-responsive transcriptome data identified three key genes, PgCDF2, PgHSFA1 and PgHSFB3, as components of the regulatory network of heat stress in P. grisea. The expression levels of PgCDF2, PgHSFA1, and PgHSFB3 were up-regulated following exposure to HS. Silencing of PgHSFA1 and PgHSFB3 resulted in reduced heat stress tolerance and altered reactive oxygen species levels in P. grisea. Dual-luciferase assay and Electrophoretic Mobility Shift Assay (EMSA) results indicate that PgCDF2 binds to the promoters of PgHSFA1 and PgHSFB3 and activate their expression. Silencing of PgCDF2 inhibited the expression of PgHSFA1 and PgHSFB3 and also reduced the heat tolerance of P. grisea. In summary, under HS, PgCDF2 enhances the heat tolerance of P. grisea by activating the expression of PgHSFA1 and PgHSFB3. This study clarifies the role of the PgCDF2-PgHSFA1/PgHSFB3 module in the response of P. grisea to HS, providing a theoretical basis for a more in-depth analysis of the molecular mechanisms underlying this response.