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The yellow pond turtle, Mauremys mutica , is an economically important aquaculture species and is widely cultured in China because of its high value as a food and in traditional Chinese medicine, as well as being a popular pet. However, M. mutica shows poor tolerance to heat stress and frequently experiences mass mortality caused by infectious diseases during late spring and early summer, when high temperatures occur frequently and various pathogens begin to propagate rapidly. In this study, we performed a comparative transcriptome analysis of M. mutica in response to continuous heat stress (3 h, 9 h, 24 h and 48 h) at 32 °C. Compared to the control group (28 °C), a total of 813, 1488, 1856 and 2001 differentially expressed genes (DEGs) were identified in the four heat-stressed groups respectively, indicating that heat stress has a significant influence on gene expression in M. mutica and that the degree of influence gradually increases with heat stress duration. Interestingly, the immunity-associated category for the complement and coagulation cascade pathway was uniquely enriched in the latter three heat stress groups (9 h, 24 h and 48 h) and all DEGs (e.g. C3, C4, C6, C7, C8, C9 and MASP1/2) in this pathway showed down-regulation as the heat stress duration increased, suggesting that immunity continuously decreases with increased heat stress duration. These observations indicate that potential dysfunction of the immune response under heat stress may contribute to the mass mortality of M. mutica during late spring and early summer. This study provides insights into the molecular mechanisms underlying the mass mortality syndrome in M. mutica and is helpful for proposing effective strategies to alleviate the damage caused by heat stress. • The complement and coagulation cascade pathway was uniquely enriched in later three heat stress groups (9 h, 24 h and 48 h). • All DEGs in this pathway showed down-regulation as the heat stress duration increased. • Potential dysfunction of the immune responsemay contribute to the mass mortality of M. mutica during late spring and early summer. [ABSTRACT FROM AUTHOR]