Abstract: Deltamethrin (DM) has been used in aquaculture as pests defender, parasites remover, salmon delouser, ponds cleanser, and so on. The low-dose DM, less than safety concentration (SC) in surface water is ubiquitous and lasts for the whole agricultural period because of frequent use. To understand the chronic stress of deltamethrin below SC on Eriocheir sinensis intestine, this research acquired the SC as 0.190 μg/L calculated from the data of acute experiments with Turubell formula, and then investigated on juvenile E. sinensis exposed to 0, 0.024, 0.095 and 0.380 μg/L DM for 30 days. Two samples were taken from each level at 0 d and 30 d, and examined intestinal histological structures on the slices stained with H.E. and also analyzed gut microbiota based on the sequence (after DNA extraction, amplification and library construction). The main results showed that ① Histological examination showed DM damaged the intestine histological structure of juvenile E. sinensis, whose adverse effects increased with the increment of DM concentration. Exposed to DM of 0.380 μg/L, the mucosal epithelial cells were collapsed, in which the mucous layer separated from the submucous layer; the villi were destructed, in which the cuticle layer separated from the mucous layer, even intestinal glands messed up. Exposed to DM of 0.095 μg/L, some part of the mucous layers were collapsed, mucous layer cells were partly degraded, and intestinal glands were partly messed up. Exposed to both 0.024 and 0 μg/L DM, there were no observable effects. ② The gut microbiota equilibrium was broken in the intestine of E. sinensis exposed to DM of chronic concentration. Ace and Chao1 indexes decreased with the increment of DM concentration, which indicated DM decreased the microbial diversity in intestine ecology. ③ In phylum-level analysis, the beneficial bacteria was decreased and pathogenic bacteria was increased in the intestinal microbiota of juvenile E. sinensis exposed to DM below the SC. DM increased the relative abundances of Proteobacteria in 0.380 μg/L treatment (P<0.01), and Bacteroidota in 0.095 μg/L treatment (P<0.05), decreased the relative abundances of Tenericutes in 0.095 and 0.380 μg/L treatments (P<0.05), and Firmicutes in 0.024, 0.095 and 0.380 μg/L treatments (P<0.05). ④ In genus-level analysis, DM increased the relative abundances of Acinetobacter, Bacteroides, and Wolbachia in all treatments (P<0.05), even resulted in some pathogenic bacteria of Pseudomonas, Shewanella, Chryseobacterium, and Flavobacterium in 0.380 μg/L treatment. In summary, DM of SC caused E. sinensis intestine in chronic stress, which damaged the intestine histological structure, broke the equilibrium of beneficial microbiota, and increased the relative abundances of pathogenic bacteria. The calculated safety concentration is not truly safe, which indicates that real DM safety concentration for juvenile E. sinensis needs more trials in aquaculture.