Accumulation of methylmercury in rice is harmful to the health of consumers. A pot experiment was conducted to study the effects of organic fertilizer application on the accumulation of mercury and methylmercury in rice in mercury- methylmercury contaminated soil. The treatments included CK, no organic fertilizer + long term flooding; AWD, no organic fertilizer + dry/wet alternation; BOM1, rotten soybean meal (1%, w/w) + long term flooding; BOM2, rotten soybean meal (2%, w/w) + long term flooding; FOM1, rotten fish meal (1%, w/w) + long term flooding; FOM2, rotten fish meal (2%, w/w) + long term flooding. The results showed that organic fertilizer significantly increased CH₃Hg⁺ content in paddy soil: CK (10.43 μg/kg) < BOM1 (16.80 μg/kg) < FOM1 (24.10 μg/kg) < BOM2 (33.53 μg/kg) < FOM2 (38.46 μg/kg). After the application of organic fertilizers, total Hg accumulation in various rice organs were significantly different, the highest in root (2 812.83 μg/kg), followed by brown rice (336.78 μg/kg) and stem and leaf (300.44 μg/kg), the abilities to accumulate CH₃Hg⁺ by different rice organs were different: grain (180.06 μg/kg) > root (59.71 μg/kg) > stem and leaf (38.97 μg/kg). Organic fertilizers increased the content of CH₃Hg⁺ in rice grains compared with the CK treatment: BOM1 (16.1%) < FOM1 (19.3%) < BOM2 (41.5%) < FOM2(57.9%). Significant positive correlation was found between CH₃Hg⁺ concentration in rice grains and CH₃Hg⁺ content in paddy soil. This study proved organic manure can increase the accumulation of mercury and methylmercury in rice in mercury contaminated soil, and it provided scientific basis and theoretical guidance for rational fertilization.