A multi-element mineral conditioner (MMC) is a kind of slightly alkaline soil conditioner prepared by calcining a mixture of calcium or magnesium-based desulfurized flue gas residue, potassium feldspar, gypsum, dolomite, and limestone powder, rich in available K, Ca, Mg, Si, and other micronutrients. To evaluate the effect of MMC on the concentration of essential cations in red soil and in the crops grown thereon, a 4-month field experiment was conducted. By applying the MMC, the acidity of the red soil caused by weathering and chronic acid rain in Southern China can be neutralized, and the essential cations severely lacking in red soil and crops can be adequately replenished. Due to the addition of essential cations to red soil, the 1: 1 type clay mineral gradually transformed into 2: 1 type clay mineral. The grain yield was increased and the quality of rice was improved. The concentrations of Pb, Cd, Hg, and As in rice grains grown in the treated soil was significantly decreased. These results demonstrate that use of MMC can ameliorate soil and improve its fertility, reduce the reliance of crops on chemical fertilizers, raise the rice yield and improve the quality of red soil.