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The mud crab (Scylla paramamosain) is an economically important crab species that is distributed along the southern coast of China. Previously we reported that various morphological types of mud crabs differentially adapt to temperature changes. This study investigates the effects of temperature on morphs with one or two spines (Sp1 and Sp2, respectively) on the outer margin of the carpus of cheliped at a low temperature (8 °C) and a control temperature (20 °C). The hepatopancreas were the transcriptome source, and a total of 81,853 unigenes were obtained by sequencing, with an average length of 420 bp, and an N50 of 1460 bp. Of these, 22.33 % were known genes. Under low-temperature stress, there were 361 differentially expressed genes (DEGs) between the two morphs; 96 and 265 were up- and down-regulated genes, respectively. There were no DEGs between the morphs at 20 °C. Functional enrichment analysis revealed that the DEGs encoded abundant metallocarboxypeptidase activity, extracellular space, proteolysis, and sequence-specific DNA binding, and were further enriched in signal pathway components, including ubiquinone and other terpenoid-quinone biosynthesis, phenylalanine metabolism, MAPK signaling pathway, apoptosis, and other signaling pathways. The gene expressions of acid phosphatase (ACP), chymotrypsin (CHY), serine carboxypeptidase (SCP), and trypsin (TRY) under low-temperature stress were detected. The expressions of ACP, CHY, and SCP gradually decreased with time. The ACP, CHY, SCP, and TRY gene expression of the Sp1 morph was lower than that of the Sp2 morph; however, the ACP gene expression of the Sp1 morph was higher than that of the Sp2 morph at several time points. In conclusion, adaptability differences between the morphs to low-temperature stress were confirmed, which will enable the selection of cold-tolerant, high-quality varieties of mud crabs for breeding.