Overwintering is an important part of the conservation of Scylla paramamosain, and salinity has an important effect on the conservation of S. paramamosain during overwintering. Three salinities (4‰, 12‰ and 25‰) were selected as the overwintering salinities to reveal the effects of different salinities on the relevant important ions in osmotic pressure regulation, plasma cortisol, digestive enzymes, immune enzymes and amino acids of S. paramamosain during indoor overwintering. Results indicated that after overwintering, Cl‐, Na+ and the osmotic pressure of serum have the highest salinity at 25‰, and the lowest salinity at 4‰. Na+/K+‐ATPase activity and cortisol were found to increase with decreasing salinity. The activity of digestive and immune enzymes was highest at 25‰, and was the lowest at 4‰. The amount of total amino acids (TAA), umami amino acids (UAA) and essential amino acids (EAA) in 25‰ were significantly higher than in 4‰ and 12‰. After overwintering, the essential amino acid index (EAAI) in the salinity range of 12–25‰ was 54.04–59.00, compared to 48.56–54.04 in the salinity range of 4–12‰. As a result, S. paramamosain at 25‰ had higher digestion and immunity than at 4‰ and 12‰, due to requiring more energy for osmotic pressure adjustment. In addition, S. paramamosain at 25‰ had the best meat quality. The results of this study are helpful for aquaculture production for indoor overwintering of S. paramamosain.