Abstract: Scylla paramamosain is an economically important crab species mainly distribute in the southern reaches of the Yangtze River. Based on many years of breeding experience, it is speculated that different morphological populations of Scylla paramamosain have acquired different adaptations to temperature changes. In this study, Sp1 populations, with “one spine on the outer margin of the carpus of cheliped ” and Sp2 populations, with “two spines” were designated research objects, and 8℃ low temperature stress and 20℃ control groups were established. The hepatopancreas was used as a transcriptome source, and an Illumina Hiseq4000 platform was used for sequencing. A total of 81853 Unigenes were obtained by sequencing, with an average length of 420 bp, and an N₅₀ of 1460 bp. Among these, 22.33% were known genes. Screening for differentially expressed genes identified 15773 Unigenes displaying significant differential expression in the Sp1 population under low temperature stress. Of these, 15628 Unigenes were down-regulated, and 145 Unigenes were up-regulated. Functional enrichment analysis revealed that the differentially expressed genes encode abundant cytosolic, RNA binding, and ribosome structural constituent proteins, and were further enriched in signal pathway components including ribosome, spliceosome, and protein processing components in the endoplasmic reticulum. 323 Unigenes were significantly differentially expressed in the Sp2 population under low temperature stress, of which, 209 Unigenes were down-regulated, and 114 Unigenes were up-regulated. Functional enrichment analysis revealed that the differentially expressed genes include abundant contributors to steroid hydroxylase activity, DNA integration, and bicarbonate transmembrane transporter activity, and were also enriched in signal pathways including lysine degradation, glycine, serine, and threonine metabolism, and arginine and proline metabolism. The above results indicated that as water temperature droped from 20℃ to 8℃, expression of a large number of genes was down-regulated in the Sp1 population, and physiological activities were drastically reduced. This may correspond to winter behaviors of Scylla paramamosain, including fasting and dwelling in burrows. By contrast, the Sp2 population mainly adjusted its material metabolism, indicating that the Sp2 population was relatively slow to respond to sudden temperature drops. Transcriptome data has been verified by RT-qPCR, supporting the feasibility of comparing responses of two morphological populations to low temperature stress based on transcriptome analysis. This study will inform selection of cold-tolerant and high-quality varieties for breeding of Scylla paramamosain.