Mercury (Hg) bioaccumulation in rice poses a health issue for rice consumers. In rice paddies, selenium (Se) can decrease the bioavailability of Hg through forming the less bioavailable Hg selenides (HgSe) in soil. Rice leaves can directly uptake a substantial amount of elemental Hg from the atmosphere, however, whether the bioaccumulation of Hg in rice leaves can affect the bioaccumulation of Se in rice plants is not known. Here, we conducted field and controlled studies to investigate the bioaccumulation of Hg and Se in the rice-soil system. In the field study, we observed a significantly positive correlation between Hg concentrations and BAFs of Se in rice leaves (r2 = 0.60, p < 0.01) collected from the Wanshan Mercury Mine, SW China, suggesting that the bioaccumulation of atmospheric Hg in rice leaves can facilitate the uptake of soil Se, perhaps through the formation of Hg-Se complex in rice leaves. This conclusion was supported by the controlled study, which observed significantly higher concentrations and BAFs of Se in rice leaf at a high atmospheric Hg site at WMM, compared to a low atmospheric Hg site in Guiyang, SW China.