In order to explore the effects of pond and paddy culture modes on the intestinal microbiota, immunity and muscle flavor of Eriocheir sinensis, the intestinal flora, immune enzyme activity and muscle free amino acids of Eriocheir sinensis from the same batch of ponds and paddy fields were measured in May and October. The results showed that the dominant intestinal flora of Eriocheir sinensis were Firmicutes, Bacteroidetes, Proteobacteria and Firmicutes. In the case that both season and breeding mode had an effect on the intestinal microbiota of crabs, and the seasonal change had a greater effect on the flora change. From May to October, the richness and diversity of intestinal microbiota of Eriocheir sinensis in paddy field culture showed an increasing trend, but there was no significant change in the richness and diversity of intestinal microbiota in pond culture. The enzyme activities of SOD in May were higher than those in October in the two modes. In October, the immune enzyme activities of LZM and ACP in pond mode were significantly higher than those in paddy field mode. The total sweet amino acid content (TSAA)> total bitter amino acid (TBAA)> total umami amino acid (TUAA) was detected in muscle of all groups. The TSAA and total free amino acid TFAA in muscle of Eriocheir sinensis under pond culture were higher than those under paddy field culture. Therefore, compared with the paddy field culture, Eriocheir sinensis cultured in pond culture mode has more stable intestinal microbiota in terms of time, stronger immune enzyme activities, and better muscle flavor.