The effects of the overwintering temperature (8, 12, 16, and 20 °C) on survival, antioxidant capacity, and heat shock protein (HSP) gene expression in Scylla paramamosain were examined during an experimental period of eight weeks. The effects of the temperature on survival were parabolic, with the highest and lowest survival rates occurring at 16 °C and 8 °C, respectively. Histological examination of the hepatopancreas revealed that the hepatopancreas tissue structure remained intact and that cell boundaries were clearly observed at 16 °C and 20 °C. However, hepatopancreas cells in the 12 °C and 8 °C groups appeared to be vacuolated and indistinct, respectively. Furthermore, high levels of reactive oxygen species (ROS) and malondialdehyde (MDA) and low levels of total antioxidant capacity (T-AOC) and superoxide dismutase (SOD) in the hepatopancreas were observed in the 8 °C group. Hsp60 and hsp70 gene expression were dramatically upregulated, but hsp10, hsp40, hsp90, and glucose regulatory protein 78 (grp78) gene expression were downregulated at 8 °C. The terminal deoxynucleotidyl transferase deoxy-UTP nick end labeling (TUNEL) method showed that there was more DNA damage at 8 °C and 12 °C than at 16 °C. Moreover, apoptosis was significantly induced with decreasing temperature, and the 8 °C group had the highest apoptosis index. Overall, these results suggest that the overwintering temperature greatly impacts the survival of mud crabs and that these effects may be mediated through antioxidant, HSP response, and apoptosis pathways. Significantly, the optimal overwintering temperature for S. paramamosain was extrapolated to be 14.2–16.1 °C. This suggests that temperature control should be considered in the process of mud crab overwintering.