The mud crab (Scylla paramamosain) is among the most economically important seawater crustacean species. Overwintering is one of an important stage for aquatic animals, and light intensity has an important effect on the conservation of Scylla paramamosain during overwintering. Here, S. paramamosain were exposed to three different light intensities (0, 1.43 and 40.31 μmol m−2 s−1) for four months. Then, GC‐MS‐based metabolomic analyses of the hepatopancreas were performed to assess differences in the metabolites produced by S. paramamosain exposed to different light intensities. The weight gain rate (WGR) was also compared among treatment groups. The LL group displayed significantly greater WGRs than the HL group. A total of 117 and 128 significantly different metabolites (SDMs) were identified in LL group and HL group respectively (VIP > 1 and p < .05). The identified SDMs were associated with the amino acid metabolism, the carbohydrate metabolism, the fatty acid metabolism, the nucleotide metabolism and membrane transport. The results suggested that light intensity affected the metabolic pathways in S. paramamosain by influencing the citrate cycle (TCA cycle), the biosynthesis of amino acids and unsaturated fatty acids, ABC transporters, and the purine metabolism. Further integrated analyses of key metabolic pathways showed that the metabolism of S. paramamosain was more vigorous under light conditions.