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The alkaline mineral amendment is a practical means of alleviating Cd concentration in rice grain (Cd R) in the short-term; however, the long-term remediation effect of mineral amendment on the Cd R and the eco-environmental controls remains unknown. Here a mineral (Si–Ca–Mg) amendment, calcined primarily from molybdenum tailings and dolomite, was applied biannually over 6 years (12 seasons) to acidic and moderately Cd-contaminated double-rice cropping ecosystems. This study investigated the inter-annual variation of Cd in the rice-soil ecosystem and the eco-environmental controls in subtropical rice ecosystems. Cd R was reduced by 50%–86% following mineral amendment. The within-year reduction in Cd R was similar between early rice (50%–86%, mean of 68%) and late rice (68%–85%, mean of 74%), leading to Cd R in all early rice and in 83% of late rice samples below the upper limit (0.2 mg kg−1) of the China National Food Safety Standards. In contrast, the inter-annual reduction in Cd R was moderately variable, showing a greater Cd R reduction in the later 3 years (73%–86%) than in the former 3 years (54%–79%). Three years continuous mineral amendment was required to guarantee the safety rice production. The concentrations of DTPA-extractable and exchangeable Cd fractions in soil were reduced, while the concentration of oxides-bound Cd was increased. In addition, the soil pH, concentrations of Olsen-P and exchangeable Ca and Mg were elevated. These imply a lower apparent phytoavailability of Cd in the soil following mineral amendment. An empirical model of the 3-variable using soil DTPA-Cd, soil Olsen-P, and a climatic factor (precipitation) effectively predicted temporal changes in Cd R. Our study demonstrates that Cd phytoavailability in soil (indexed by DTPA-extractable Cd) and climatic factors (e.g., temperature and precipitation) may directly/indirectly control the inter-annual reduction in Cd R following mineral amendment in slightly and moderately Cd-contaminated paddy ecosystems. [Display omitted] • Continuous mineral amendment (MA) in mild Cd-contaminated paddy immobilized Cd. • Three years continuous MA was required to guarantee safety rice production. • Inter-annual reduction of rice Cd (Cd R) was variable in 6-year biannual MA. • Cd R reduction was similar in early and late rice. • Temporal Cd R was effectively predicted by soil DTPA-Cd, Olsen-P, and precipitation. [ABSTRACT FROM AUTHOR]