Methylmercury (MeHg) in rice grains grown in Hg-contaminated areas has raised environmental health concerns. Pot experiments found that selenium (Se) could reduce MeHg levels in rice grains. However, relatively high levels of Se (up to 6 mg/kg) were applied in these pot experiments, which may have adverse effects on the soil ecology due to the toxicity of Se. The aims of this work were thus to study 1) the effect of low levels of Se on the accumulation and distribution of Hg, especially MeHg, in rice plants grown in a real Hg-contaminated paddy field and 2) the effect of Se treatment on Se and other nutritional elements (e.g., Cu, Fe, Zn) in grains. A field study amended with different levels of Se was carried out in Hg-contaminated paddy soil in Qingzhen, Guizhou, China. The levels of MeHg and total Hg were studied using cold vapor atomic fluorescence spectrometry (CVAFS) and inductively coupled plasma mass spectrometry (ICP-MS). The distribution and relative quantification of elements in grains were examined by synchrotron radiation X-ray fluorescence analysis (SR-XRF). This field study showed that low levels of Se (0.5 μg/mL, corresponding to 0.15 mg Se/kg soils) could significantly reduce total Hg and MeHg in rice tissues. Se treatment also reduced Hg distribution in the embryo and endosperm and increased the levels of Fe, Cu, Zn and Se in grains and especially embryos. This field study implied that treatment with an appropriate level of Se is an effective approach to not only decrease the level of MeHg but to also increase the levels of nutritional elements such as Fe, Cu, Zn and Se in rice grains, which could bring beneficial effects for rice-dependent residents living in Hg-contaminated areas.