<p>Tomato, one of the most important vegetable crops around the world, is sensitive to heat stress. Identifying heat-tolerant genes and breeding resilient varieties are vital for addressing the challenges of global warming and ensuring food security. In this study, we compared seedlings of a cultivated tomato accession (<i>Solanum lycopersicum</i>, M82) with those of a wild accession (<i>S. pimpinellifolium</i>, LA1589) at both physio-biochemical and transcriptomic levels under a 42℃ heat treatment. Various physio-biochemical indicators demonstrated that LA1589 exhibited superior heat tolerance compared to M82 at the seedling stage. We conducted dynamic transcriptome analyses of these two genotypes under heat treatment, identifying 10,681 differentially expressed genes (DEGs) in LA1589 and 10,462 DEGs in M82. Among these, 1,857 genes were specifically up-regulated and 1,228 genes were specifically down-regulated in LA1589, while 1,916 genes were specifically up-regulated and 1,021 genes were specifically down-regulated in M82. The enrichment analyses indicated that DEGs were significantly clustered in biological processes and pathways associated with heat resistance. Notably, the specifically down-regulated genes in LA1589 were significantly enriched only in the plasma membrane pathway, whereas in M82, these genes were enriched in chloroplast-associated processes and other pathways. Weighted gene co-expression network analysis identified heat-response modules, including TM11, PM3 and PM23. Further analysis revealed the involvement of <i>SlHsfA7</i>, heat shock proteins and chloroplast-related genes in the center of the heat-responsive regulatory network in tomato. Our findings provide a solid foundation for further functional elucidation of candidate heat-tolerant genes and their underlying molecular mechanisms in tomato.</p>