In this study, pot experiments were conducted with a blank control (CK), a mercury (Hg) control prepared by adding exogenous Hg in soil over one month-long aging, and three organic material treatments including rape straw, pig manure and rice straw biochar at a dosage of 3% (m/m) to Hg-amended soil aged as the Hg control, respectively. The effects of application of different organic materials were compared on rice yield and Hg migration and transformation in paddy field system. The results showed that the application of the three kinds of organic materials significantly increased rice yield, but the effects on Hg methylation in soil and Hg accumulation in brown rice were not consistent. Compared with the blank control, rice yield was increased by 17.6%, 33.0% and 39.9% under the treatments of rape straws, pig manure and rice straw biochar, respectively. Compared with the Hg control, the application of pig manure increased the bioavailability of Hg in soil and promoted methylmercury (MeHg) production and the bioaccumulation factor of total mercury (THg) in brown rice, with the concentrations of THg and MeHg in brown rice being increased by 34.5% and 30.3%, respectively. However, the application of rape straws reduced Hg bioavailability in soil and inhibited the methylation of Hg in soil and the bioaccumulation of Hg in brown rice, with the concentrations of THg and MeHg in brown rice being decreased by 34.6% and 36.2%, respectively. Hg bioavailability in soil and the bioaccumulation factor of THg in brown rice were decreased by applying rice straw biochar, and THg and MeHg content in brown rice were decreased by 46.9% and 48.4%, respectively. Therefore, application of rice straw biochar and rape straw is potential measure to achieve the dual effects of increasing rice yield and preventing Hg accumulation in brown rice in Hg contaminated paddy fields, while pig manure is not recommended.