Cadmium (Cd) contamination in rice paddy fields constitutes a serious health issue in some parts of China. Here we study the potential for remediation of Cd contaminated alkaline paddy soil with low Fe and high Cu background by altering the concentrations of iron (Fe) and copper (Cu) in the growing media, which has been only seldom considered. We assessed how these two micronutrients (Cu and Fe) affect the absorption and transport of Cd in rice. Adding Cu significantly increased rice biomass and grain yield by reducing root Cd influx and Cd upward transport which, consequently, lowered Cd concentrations in roots, culms and leaves. However, excessive Cu also promoted a relatively higher Cd allocation in grains, especially under Fe deficiency, likely because Cu significantly increased the proportion of bioavailable Cd in leaves. Contrastingly, Fe did not alleviate the toxic effects of Cd on rice growth and yield, but it significantly reduced Cd transfer towards grains, which might be attributed to a sharp decrease in the proportion of bioavailable Cd in leaves. Our results demonstrated that Cd remediation may be achieved through altering Fe and Cu inputs, such that Cd accumulation in rice grains is reduced.