Silicon (Si) is the second most abundant element in the earth’s crust, the beneficial effects of this element on the growth, development, yield and disease resistance have been observed in a wide variety of plant species. However, the precise distribution of silicon, and its relationship with some heavy metals in oat grain are largely unexplored. In the present study, the Si levels of 22 oat genotypes in 4 different grain parts (the cortex, aleuronic layer, near aleuronic layer and center of caryopsis) were determined by environmental scanning electron microscopy combining with X-ray electron probe microanalysis, and its relevancy with the contents of other metals in the whole oat grain, including P, Mg, K, Ca, S, Cd, Al and Pb, were analysed. There was remarkable difference in Si levels among different portions of oat grain, with higher Si contents in the cortex and aleuronic layer, while less Si in the near aleuronic layer and center of caryopsis, which implied that Si predominantly deposited in the aleuronic layer for a whole oat caryopsis. Moreover, the considerable difference in Si level was also existed among the different oat genotypes, with a comparison of the same portion of different oat cultivars, suggesting that oat genotypes had a dominant effect on Si accumulation. Si content in aleuronic layer was closely related to that in near aleuronic layer and center of caryopsis. Furthermore, a significant non-linear correlation between the content of Si and that of P, Ca, Mg, S, Al, Pb in different parts of oat grains was observed, but no significant non-linear relationship existed between the content of Si and that of K、Cd in the center of caryopsis. The Si accumulation might facilitate the accumulation of P, Ca, Mg, S, Al and Pb.