A previous investigation had demonstrated that mineral element (Fe, Mn, Cu, Zn, Ca and Mg) concentrations in brown rice of indica IIY084 and japonica WYJ23 (Oryza sativa L.) were significantly reduced by elevated [CO₂]. However, the underlying mechanisms were still unclear. Thus, a field experiment was conducted to investigate mineral element partitioning and rhizosphere availability of IIY084 and WYJ23 with a Free-air CO₂ Enrichment (FACE) in Eastern China. The results showed that regardless of cultivars, the biomass of panicles, stems, roots and whole plants were significantly stimulated by elevated [CO₂] with average increase of 19.4%, 9.3%, 23.4% and 16.0%, respectively. Generally, elevated [CO₂] trended to raise the bio-available contents of mineral elements in the rhizosphere soils. Except for the enhanced accumulation of Ca, most of mineral element accumulations in the whole plants were unchanged under elevated [CO₂]. However, elevated [CO₂] significantly increased the uptake and distribution of mineral element in panicles but declined them in stems. Interestingly, most of mineral elements distributed in husk and stalk were detained, while those in brown rice were reduced by elevated [CO₂]. In the case of cultivar effects, the biomass of stems and whole plants, the accumulation and distribution of Fe, Mn and Cu in panicles, Zn and Mg in leaves, and Cu in stems were much greater in IIY084 than in WYJ23. However, the accumulation and distribution of Mn in leaves, Fe in stems and Cu, Zn in roots showed an opposite trend. In short, the mineral element decline in brown rice may mainly attribute to the unbalanced stimulations on the translocations of mineral elements and carbohydrates from vegetative parts to the grains under elevated [CO₂], as well as to more retention in husks and stalks of rice panicles.