Recent studies indicate elevated methylmercury (MMHg) production and bioaccumulation in soil-rice systems, raising health concerns. However, mechanistic understanding about key factors controlling Hg methylation and thus risk of MMHg in rice paddy fields are lacking. We explored the controls of key factors on Hg methylation and bioaccumulation in contaminated soil-rice systems: (1) Rice straw amendment could largely enhance Hg methylation in paddy soils and thus MMHg accumulation in rice plants; (2) Biochar amendment would largely reduce phytoavailability and thus bioaccumulation of MMHg (49–92% in rice grain), while enhance Hg methylation in soils; (3) Se amendment into soils could significantly reduce Hg methylation in soils, by forming refractory Hg-Se complexes (XANES analysis), which in turn reduced MMHg accumulation in rice plants. In contrast, Se accumulation in plants could have minor effects on reducing MMHg accumulation in rice; (4) Humus-coated clay could largely decrease Hg bioavailability; (5) Bioavailability of inorganic mercury (IHg) and MMHg decreased sharply within short period of Hg-soil contact (2-28 days), while the reduction was more evident in soils with lower organic content. The effects of those key factors on Hg methylation and bioaccumulation, as well as the mechanistic explanation, improve our understanding about Hg dynamics and risk in contaminated soil-rice systems.