<p>The circadian rhythms of gut bacterial community are essential for the health of the host. Although previous studies have shown that environmental light cycles synchronize circadian feeding patterns in animals and regulate microbial communities through environmental fluctuations, the role of light in regulating the circadian rhythms of gut bacterial community in crustaceans and the impact of dark environments on these rhythms remain unclear. To address this issue, we used the mud crab (<i>Scylla paramamosain</i>) as a model to evaluate the circadian rhythms of gut bacterial community in different photoperiods (12-h L:12-h D and 0-h L:24-h D), and identified the microbes exhibiting circadian rhythms influenced by light exposure and microbial circadian clocks. The study found that 12-h L:12-h D photoperiod optimally supports mud crab growth performance, animal welfare, and circadian microbial balance. While gut microbiota exhibited rhythmic fluctuations in different photoperiods, the community composition analysis revealed significant differences between light/dark and continuous dark conditions. The circadian rhythmic microbes regulated by light exposure were primarily dominated by Spirochaetes, while the dark environment significantly reduced the relative abundance of Alpha-proteobacteria and Bacteroidetes (<i>P</i>&lt;0.05), with Fusobacteria serving as a representative microorganism. Additionally, the dark environment caused significant fluctuations in functional pathways related to environmental stress response (<i>P</i>&gt;&lt;0.05), such as the FoxO signaling pathway, lysosome, and RNA transport, suggesting that a complete darkness environment disrupts the biological clock. These findings elucidated the regulatory mechanisms of circadian rhythms in the gut bacterial community of mud crabs and highlighted the significant role of light in shaping gut bacterial community.</p>