Abstract: To investigate the effects of decreased water temperature during the fattening period on the bacterial community structure in multiple tissues of female Eriocheir sinensis, 90 female crabs that had completed reproductive molt were randomly divided into a normal water temperature group (25℃) and a low-temperature group (18℃), with three replicates per group and 15 crabs per replicate. After a 45-day experimental period, the composition, diversity, functional characteristics, and cross-tissue migration patterns of bacterial communities in the hemolymph, intestine, hepatopancreas, and ovary tissues were systematically characterized using 16S rRNA gene high-throughput sequencing. The results showed that compared with the control group, the low-temperature group did not significantly affect the α-diversity indices of bacterial communities in the intestine, hemolymph, hepatopancreas, or ovary, but significantly reduced the relative abundance of Bacteroidetes and increased the Firmicutes/Bacteroidetes ratio across multiple tissues. In addition, the low-temperature group significantly reduced the relative abundance of potential pathogenic genera (e.g., Anaerovorax, Arcobacter, Enterococcus) in multiple tissues. Compared with bacteria communities in other tissues, low temperature primarily inhibited the overall metabolic activities of intestinal bacteria, including those involved in carbohydrate, lipid, energy, and vitamin metabolism. Bacterial network analysis revealed that low temperature reduced the complexity of bacterial networks in the intestine, hepatopancreas, and hemolymph, but specifically increased complexity in the ovary. Across all tissues, Proteobacteria, Bacteroidetes, Tenericutes, and Firmicutes were the dominant bacterial phyla. The bacterial community structures in the hepatopancreas and ovary were distinctly different from those in the hemolymph and intestine. The hemolymph selectively enriched beneficial bacteria, such as Rhodobacter and Arthrobacter, while inhibiting opportunistic pathogens, including Vibrio and Citrobacter. Source tracking analysis revealed that the intestine was the primary source of hemolymph bacteria, and the hemolymph mediated bacterial transfer to the hepatopancreas and ovary. Moreover, the low-temperature group significantly reduced the proportion of bacterial transfer from hemolymph to hepatopancreas and ovary. In conclusion, this study indicates that reduced environmental temperature during the fattening period can optimize the bacterial community structure in multiple tissues of female crabs, suppress the relative abundance of pathogens, and provide a favorable physiological environment for ovarian development. These findings provide a theoretical basis for optimizing water temperature management and regulating reproductive development in Eriocheir sinensis aquaculture.