As one of the essential nutrient elements in plant, calcium, accounting for about 2 percent of body weight in rice plant, is the important component in cell wall formation, and participates in the most of metabolism process, such as growth, pollination and fertilization, regulation of enzyme activity, stress resistance, and the signal conduction. However, the precise distribution of calcium, and its relationship with some heavy metals in rice grain are largely unexplored. In the present study, the Ca levels of 21 rice genotypes in 6 different grain parts were determined by environmental scanning electron microscopy combining with X-ray electron probe microanalysis (the inner and outer surface of rice glume, surface of caryopsis, center of caryopsis, near aleuronic layer and aleuronic layer), and its relevancy with the contents of other metals in whole a rice grain, including P, Mg, K, Si, Cd, Al and Pb , were investigated. The results showed that there was remarkable difference in Ca levels among different portions of rice grain, with higher Ca levels in the inner and outer surface of rice glume, and the surface of caryopsis, while less Ca amounts in the near aleuronic layer and center of caryopsis, implying that Ca predominantly located in the aleuronic layer for a whole rice caryopsis. Moreover, the considerable differences in Ca level were also existed among the different rice genotypes, with a comparison of the same similar portion of different rice cultivars, suggesting that rice genotypes had a dominant effect on Ca accumulation. Ca content in aleuronic layer was closely related to those in outer surface of rice glume, surface and center of caryopsis and near aleuronic layer of rice grains. In addition, there were significant non-linear correlations between the content of Ca and that of P, Mg, K, Si, Al, Cd in different parts of rice grains, but no significant non-linear correlations existed between the content of Ca and Pb. That was, the Ca accumulation could facilitate the accumulation of P, Mg, K and Si. However, Ca might also enhance Al and Cd accumulation in rice grains, which have potential toxicity to human beings.