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Heat stress poses a significant constraint on the annual production of L. edodes, a challenge that has been intensified by global warming. Previous studies have established a close relationship between intracellular IAA content and heat tolerance in L. edodes. However, the specific changes in the IAA synthesis pathway and the target genes regulated by IAA under heat stress remain unclear. We employed targeted metabolomics and transcriptomics analysis to investigate the alterations in IAA synthesis pathways and gene expression in both heat-tolerant and heat-sensitive strains at various time points during heat stress. Our findings revealed that IAA is primarily synthesized via the TAM and IPYA pathways in L. edodes. Heat-sensitive strain Y3357 exhibited excessive accumulation of tryptamine after heat stress. Silencing of the key genes of IAA synthesis include tryptophan decarboxylase (TDC) and tryptophan transaminase (TAA) in strain S606 could reduce the thermotolerance of L. edodes mycelia. Transcriptome analysis revealed that heat-tolerant strain S606 had an earlier response to protein folding and mitochondrial gene expression compared to the heat-sensitive strain Y3357. Additionally, most genes in the MAPK signaling pathway were up-regulated after 10-24 hours of heat stress, with auxin response elements (AREs) identified in their promoters. These results suggest that the excessive tryptamine accumulation is the newly discovered limiting factor for thermotolerance, and the expression levels of key genes in the IAA synthesis pathway could directly influence hyphal thermotolerance. This study provides a new perspective on the mechanism by which IAA and its synthesis precursors affects thermotolerance of L. edodes.