Photoperiod is one of the most important environmental cues for the organism, and it plays a critical role in regulating organisms' survival, growth, and metabolism. In the present study, the effects of photoperiod (0 L∶24 D, 6 L∶18 D, 12 L∶12 D, 18 L∶6 D, and 24 L∶0 D) on mortality, growth performance, and lipid metabolism of juvenile mud crab (Scylla paramamosain) were studied with an 8-week experiment. The results showed that the highest final weight of crabs was observed in the 18 L∶6 D (0.48 ± 0.08 g), which was significantly higher than 0 L∶24 D (0.22 ± 0.03 g) and 6 L∶18 D (0.28 ± 0.04 g) (P < 0.05). In addition, the specific growth rate (SGR) of crabs reared at 12 L∶12 D (natural photoperiod) (5.83 ± 0.26% day−1) and 18 L∶6 D (6.28 ± 0.27% day−1) were significantly higher than 0 L∶24 D (4.70 ± 0.42% day−1), 6 L∶18 D (5.16 ± 0.22% day−1) and 24 L∶0 D (5.60 ± 0.23% day−1) (P < 0.05). The survival rate of the natural photoperiod group was significantly higher than 18 L∶6 D group (69.23 ± 6.28% vs 35.90 ± 3.63%) (P < 0.05), but no significant difference between 0 L∶24 D (58.97 ± 3.63%), 6 L∶18D (66.67 ± 7.25%) and 24 L∶0 D (58.97 ± 7.25%) groups was observed (P > 0.05). Crabs exposed to 18 L∶6 D photoperiod also had higher melatonin (311.12 ± 79.53 pg mL−1 vs 168.79 ± 31.24 pg mL−1) and cortisol levels (451.37 ± 237.64 ng mL−1 vs 112.91 ± 39.32 ng mL−1) than those reared in constant light (24 L∶0 D) (P < 0.05). In addition, compared with natural photoperiod, crabs reared under constant darkness showed significantly higher TG and TC content (P < 0.05). Moreover, in constant darkness, lipogenesis-related genes such as fatty acid synthase (fas), sterol regulatory element binding protein-1 (srebp-1), and acetyl-CoA carboxylase (acc) of the crab were up-regulated, and lipolysis-related genes as carnitine palmitoyltransferase-1 (cpt-1), Acyl-CoA oxidase-3 (aco-3) were significantly down-regulated (P < 0.05). Besides, fatty acid binding protein (fabp) was also up-regulated in crabs reared under constant darkness. Thus, these results suggest that the crabs in constant darkness did not effectively utilise the lipid as an energy source. Overall, the present research confirmed that light cues are indispensable for the indoor mud crab culture system, and the natural photoperiod was recommended for mud crab during the juvenile grow-out phase in commercial operations.