Adding limestone into acidic paddy soils might reduce cadmium (Cd) accumulation in rice plants and the harvested grains but with inconsistent results in the field practice. We conducted three experiments of different field scales, including small-plots, multi-location trial, and large-scale field samplings of rice grown in a major production region of southern China, to investigate whether liming could sustainably limit the Cd phytoavailability to rice. Forty-eight physical, chemical, and biological attributes associated with paired soils and plants were collectively analyzed. Rice Cd uptake was significantly reduced when moderate dosage (2.25–3 t ha−1) of liming was present in the soils. The limes decreased rice Cd uptake by reducing the Cd concentrations of soil solution phase and regulating Ca2+ and Cd2+ competitions for absorption sites at root surfaces. Soil Zn hardly any effect on rice Cd uptake. Rice Cd uptake was suppressed at the higher rates of liming (4.5–9 t ha−1) due to the heavy loss of soil labile Mn. The tendencies of over compensating were soil-, plant-, and climate-dependent and were estimated by a transfer function and the risks were characterized using probabilistic analysis. The sustainable doses of limestone that reduced grain Cd accumulation, but did not compromise yield, or disrupt the rice rhizosphere was 3 t ha−1 annually incorporated two weeks before the seedlings were transplanted.