Abstract: This study aims to investigate the impact of the newly established rice-Macrobrachium rosenbergii rotation system on physicochemical properties, nutrient supply capacity, and microbial diversity of reclaimed soil, and finally 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) of the rotation systme by field sampling, laboratory chemical analysis, and high-throughput sequencing. The results indicated a significant increase in the proportion of >2 mm soil aggregates in 0–20 mm compared to than in 20–40 cm soil after shrimp harvest and rice harvest (P<0.05). Soil bulk density, 0.25−2.0 mm, and <0.25 mm soil aggregates were all higher than those before shrimp stock. The soil reduction 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 contents of organic reducing substances, Fe²⁺ and Mn²⁺ after shrimp and rice harvests were significantly higher than those before shrimp harvest (P<0.05). The total and available nutrients contents in the 0–20 cm soil layer were higher than those in the 20–40 cm soil layer. Furthermore, the contents of soil organic matter and total and available nutrients followed the order: after shrimp harvest > after rice harvest > before shrimp stock. Additionally, the contents of organic matter, total nitrogen, and total phosphorus in the soil after shrimp harvest were significantly higher than those before shrimp stock (P<0.05). The number of operational taxonomic units after shrimp and rive harvests was significantly higher than that before shrimp stock (P<0.05). Hence, the newly established rice-M. rosenbergii rotation model is advantageous for enhancing the physical structure of topsoil, boosting soil buffer capacity, increasing nutrient supply, and enhancing microbial diversity. However, while the improvement effects were more pronounced in the 0–20 cm surface layer than in the 20–40 cm soil layer, there is also a potential risk of soil secondary compaction. The findings of this study serve as a theoretical foundation for optimizing rice and shrimp farming strategies to maximize economic and ecological benefits.