Abstract: To investigate the impacts of the newly established rice-macrobrachium rosenbergii rotation system on reclaimed soil physicochemical properties, nutrient supply capacity, and microbial diversity, and finally in order to objectively evaluate the comprehensive economic and ecological benefits of this system. This study examined the physical properties, reducing substances, total and available nutrients, and microflora structure of soil layers (0−20 cm and 20−40 cm) at three different production stages (before shrimp stock, after shrimp harvest, and after rice harvest) using field sampling, laboratory chemical analysis, and high-throughput sequencing methods. The results indicated a significant increase in the proportion of >2 mm soil aggregates from top to bottom after shrimp and rice harvesting (P<0.05). Soil bulk density, 0.25−2.0 mm, and <0.25 mm soil aggregates were all higher compared to those before shrimp stock. The soil reducing index in the 20~40 cm layer after shrimp harvest was significantly higher than that in the 0−20 cm layer (P<0.05). Additionally, the levels of organic reducing substances, Fe²⁺, and Mn²⁺ after shrimp and rice harvest were significantly higher than those before shrimp harvest (P<0.05). Total and available nutrients in the 0−20 cm soil layer were higher than those in the 20−40cm soil layer. Furthermore, the levels of soil organic matter, total and available nutrients followed the order: after shrimp harvest > after rice harvest > before shrimp stock. Additionally, the levels of organic matter, total nitrogen (TN), and total phosphorus (TP) in soil after shrimp harvest were significantly higher than those before shrimp stock (P<0.05). The number of Operational Taxonomic Units (OTUs) at 0−20 cm depth after shrimp harvest was significantly higher than that before shrimp harvest (P<0.05). Hence, the newly established rice-macrobrachium rosenbergii rotation model is advantageous in enhancing the physical structure of the topsoil, boosting soil buffer capacity, increasing nutrient supply, and enhancing microbial diversity. However, while the improvement effects are more pronounced in the 0−20 cm surface layer compared to the 20−40 cm soil layer, there is also a potential risk of soil secondary compaction. The findings of this study will serve as a theoretical foundation for optimizing rice and shrimp farming strategies, further aiming to maximize their economic and ecological benefits.