Three types of paddy soils, derived from granite, Quaternary red clay and basalt, respectively, were selected to study the effects of Fe and Mn in paddy soils on methane production and emission through pot and incubation experiments. The results indicated that the difference of Fe and Mn in paddy soils was one of the important factors causing obvious differences in methane emission from different soil types. Soil Fe and Mn affecting methane emission from the paddy soils was likely through affecting soil Eh and forming Fe and Mn plaques on rice roots. Different rates and valences of added Fe and Mn significantly affected methane production from paddy soils. Therefore, this study enhanced understanding of processes controlling methane emission from paddy soils and may help to improve modeling and estimating regional and global methane emission from paddy soils.