Consumption of rice has been shown to be an important route of dietary exposure to methylmercury (MeHg, a neurotoxin) for Asians having a low fish but high rice diet. Therefore, factors that increase MeHg production and bioaccumulation in soil–rice systems, could enhance the risk of MeHg exposure. On the basis of a national-scale survey in China (64 sites in 12 provinces) and rice cultivation experiments, we report that straw amendment, a globally prevalent farming practice, could increase MeHg concentrations in paddy soils (11–1043%) and rice grains (95%). By carrying out a series of batch incubation, seedling uptake and sand culture experiments, we demonstrate that these increases could be attributed to (1) enhanced abundances/activities of microbial methylators and the transformation of refractory HgS to organic matter-complexed Hg, facilitating microbial Hg methylation in soils; (2) enhanced MeHg mobility, and increased root lengths (35–41%) and tip numbers (60–105%), increasing MeHg uptake by rice roots; and (3) enhanced MeHg translocation to rice grains from other tissues. Results of this study emphasize fresh organic matter-enhanced MeHg production and bioaccumulation, and highlight the increased risk of MeHg after straw amendment and thus the need for new policies concerning straw management.