Abstract: Cadmium (Cd) is a heavy metal which is toxic, difficult to degrade and easy to accumulate, and it has become one of the most important heavy metal pollutants in aquaculture waters. In order to investigate the toxic effects of heavy metal pollution on the early developmental stages of shrimps, we investigated the effects of cadmium stress on the structure and function of intestinal microbial communities of Macrobrachium rosenbergii seedlings. The seedlings were evenly divided into the control (C0: 0 mg·L⁻¹) and cadmium-treated groups (C1: 0.1×10⁻⁴ mg·L⁻¹ , C2: 0.3×10⁻⁴ mg·L⁻¹ , C3:0.5×10⁻⁴ mg·L⁻¹ and C4:0.7×10⁻⁴ mg·L⁻¹) and cultured for 42 d. The results show an increase in the number of operational taxonomic units (OTUs) in the cadmium-treated group compared with the control group, and a significant increase in the ACE index and Chao1 index in C4 group (p<0.05). On phylum level, the dominant flora in C0–C4 groups were Firmicutes, Proteobacteria and Actinobacteriota, and on genus level the dominant flora in C0–C4 groups was Lactococcus. Besides, there were significant differences on phylum level between Bacteroidota and Patescibacteria in C4 group, and on genus level between Pseudoxanthomonas and Sporocytophaga in C4 group (p<0.05). A total of 51 significantly different marker species were found in the five groups by LEfSe analysis. KEGG analysis reveals that the functions of intestinal flora after cadmium stress mainly focused on metabolic-like pathways such as carbohydrate metabolism, amino acid metabolism and energy metabolism. The study shows that cadmium changed the structural composition and functional characteristics of the intestinal flora of M. rosenbergii seedlings, which helps to further optimize the breeding mode, reduce the losses caused by cadmium pollution, and ensure the stable development of M. rosenbergii aquaculture industry.