This study aims to analyze the dynamic changes of intestinal microbiome in female Scylla paramamosain from the southeast coastal China during the overwintering period （ΔT≥10℃）， and to reveal the changes in gut bacterial structure during the natural overwintering process. Intestinal samples （n=18） were collected before （November， 20 ℃）， during （January， 8 ℃） and after （March， 18 ℃） overwintering. High-throughput sequencing of the V3-V4 region of the 16S rRNA gene was performed. The richness and diversity of the microbiota structure were systematically evaluated. The results showed that a total of 1 500 137 high-quality and effective sequences were detected in the three groups of samples， which belonged to 2 518 OTUs. The highest number of OTUs was observed during overwintering， and the intestinal microorganisms of S. paramamosain shared 164 OTU in the three periods. The dominant phylum was Firmicutes and the dominant genus was Candidatus Hepatoplasma before overwintering， and the dominant phylum， genus was Spirochaetota， Sediminispirochaeta during overwintering. After overwintering， the dominant phylum was Bacteroidota， and the dominant genus was Sediminispirochaeta. The Alpha diversity analysis of the intestinal microbial community at different stages showed that the abundance and species diversity in the overwintering were higher than before and after overwintering. Evenness analysis showed that the distribution of intestinal microbial species was the lowest uniformity in overwintering， and the evenness of intestinal microbial species was the most before overwintering. The flora before overwintering was obviously different from that in the middle and late stages of overwintering. LEfSe analysis showed that probiotics can be developed during overwintering， but they need to be verified. During the overwintering period， the overall metabolism of S. paramamosain is enhanced， including carbohydrate metabolism in the early stage， lipid and amino acid metabolism in the middle and late stages， and the functional expression of stress-related genes is up-regulated in the middle and late stages， which may lead to the increased resistance of S. paramamosain during the overwintering period. This is the first study to systematically reveal the composition， diversity， and functional changes of the gut microbiota in S. paramamosain during overwintering， which provides a theoretical basis for the development of overwintering management strategies for S. paramamosain based on gut microbiota.