Abstract:[Objective] To explore the effects of rice-crab co-culture on physicochemical indicators and microbial community structure of soil in the Yellow River irrigation area of Ningxia and thus provide a theoretical basis for promoting rice-crab farming in the Yellow River irrigation area in northwest China. [Methods] The physicochemical indicators of soil were measured, and high-throughput sequencing of 16S rRNA gene amplicons was employed to reveal the microbial community structure in the fields with only rice planting (CK) and rice-crab co-culture (EG) by introduction of crabs into the ditches around rice plots. [Results] EG had higher soil pH, total nitrogen (TN), and soil organic matter (SOM) and lower total salt content than CK from April to August. The TN, available phosphorus (AP), and SOM in EG were significantly higher than those in CK in June and July. In terms of microbial community structure characteristics, EG significantly altered the bacterial community structure in soil, increasing the bacterial diversity and abundance in April, and August. EG had higher cumulative relative abundance of the top 20 bacterial phyla than CK from April to August. The dominant phylum of both CK and EG from April to August was Proteobacteria. At the genus level, EG increased the relative abundance of Pseudomonas and decreased the relative abundance of Thiobacillus and Methanosaeta. The comparison showed that EG had stronger effect on the bacterial community structure than the sampling month. Correlation analysis shows that TN is the main factor affecting the relative abundance of soil bacteria, and it is significant (P<0.05). [Conclusion] Compared with traditional rice monoculture (CK), sampling rice crab intercropping (EG) enhances soil fertility, increases the relative abundance of Proteobacteria and Pseudomonas in the soil, and helps improve soil fertility and nutrient cycling efficiency, as well as clean up pollutants in soil and water bodies.