Bacterial communities are crucial to the productivity and ecosystem services of rice-crab co-culture, an ecological agricultural strategy that blends rice and crab farming. The study's sample was gathered between April and August of 2022. The bacterial community structure in soil and water samples from the paddy field was examined tilizing omics approaches and high-throughput sequencing technologies. To investigate the bacterial communities' coexistence patterns and assembly processes, a combination of non-metric multidimensional scaling (NMDS), β-diversity decomposition, community ecology models, and redundancy analysis (RDA) was employed. Proteobacteria were the most prevalent phylum in both soil and water, according to the results, which also demonstrated that the soil bacterial community was more diverse and rich than the water bacterial community. The bacterial communities' β-diversity decomposition revealed that turnover mechanisms were predominant in both soil and water. Water bacterial communities showed a greater reliance on migration, with more noticeable stochastic processes, according to the neutral community model (NCM). The NCM model yielded R² values of 0.619, 0.629, and 0.633 for bacterial communities in water and 0.638, 0.569, and 0.424 for bacterial communities in soil. According to RDA analysis, the relative abundance of soil bacteria was correlated with available phosphorus (AP), Ph, total potassium (TK), ammonia nitrogen (NH⁺₄-N), and total phosphorus (TP), whereas the relative abundance of water bacteria was primarily correlated with water temperature (WT), chemical oxygen demand (COD_Mn), alkalinity (ALK), nitrate nitrogen (NO₃-N), and electrical conductivity (EC). This work offers scientific proof for improving management and encouraging its adoption in the northwest by illuminating the principles behind the formation of soil and water bacterial populations in rice-crab co-culture systems.