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Flooding intensity significantly alters the availability of iron (Fe), zinc (Zn), and cadmium (Cd) in paddy soil. However, the influence of arbuscular mycorrhizal fungi (AMF) on the uptake and transfer of Cd and micronutrients (Fe and Zn) under Cd stress in varying flooding conditions is not well understood. A pot experiment was conducted to investigate the micronutrient homeostasis and Cd uptake and transfer in rice cultivated in Cd-contaminated soil with AMF inoculation under continuous and intermittent flooding conditions. Compared to non-inoculation controls, mycorrhizal inoculation decreased Cd concentration in rice plants under continuous and intermittent flooding, and improved grain yield by 39.2 % for early season rice and 21.1 % for late season rice under continuous flooding. Mycorrhizal inoculation balanced the availability of Zn and Fe and decreased the availability of Cd in soil, lowering the ratios of soil-available Cd to both soil-available Zn and soil Fe2+. These changes led to a redistribution of Zn and Fe concentrations in rice, thereby reducing Cd acquisition in a soil-rice system. Structural equation model (SEM) analysis revealed that mycorrhizal inoculation had a strong direct negative effect on the expression of Zn and Fe-related genes OsNRAMP1, OsIRT1, and OsIRT2 in the roots of rice, which in turn directly affected root Cd concentration. Furthermore, mycorrhizal colonization decreased Cd transfer coefficients from leaves to grains under continuous flooding and from nodes and leaves to grains under intermittent flooding. In the nodes, the Fe concentration and the expression of genes OsIRT1 and OsHMA2 were associated with Cd transfer from the nodes to grains. Similarly, in the leaves, the expression of genes OsZIP1 and OsMTP1 corresponded with Cd transfer from leaves to grains. This study provides insights into the role of AMF in affecting micronutrient concentrations and Cd uptake in rice under varying flooding conditions.