In order to provide scientific basis for rational fertilization, a field experiment was conducted to evaluate the effects of different fertilization methods on runoff nitrogen (N) and phosphorus (P) loss in double cropping paddy field. Six treatments were designed: without N (WN), chemical fertilizer (HF), pig manure alternative 20% N fertilizer (ZF), biogas slurry and biogas residue alternative 20% N fertilizer (ZYF), compost alternative 20% N fertilizer (DF), and green manure in early rice and straw in late rice alternative 20% N fertilizer (LDF). The results showed that total N, NO3-, NH4+, total P and water soluble P in runoff water were decreased after base fertilizer and topdressing application. In double cropping rice field, total N, NH4+and NO3- contents in runoff water under HF reached 5.91 mg/L, 3.65 mg/L and 0.82 mg/L respectively, which were higher than other treatments. Compared with HF, total N, NH4+and NO3- contents in runoff water were significantly decreased when chemical fertilizers were partially replaced with organic materials, and the reduction of DF reached up to 1.18 mg/L, 0.71 mg/L and 0.14 mg/L respectively. Moreover, the treatments with organic materials alternative 20% N fertilizer significantly increased total P and soluble P content in the runoff water with the exception of DF. Compared to HF, other organic-inorganic fertilizers treatments decreased runoff N loss. In addition, total N, NH4+and NO3- loss of DF treatment was 10.25 kg/hm2, 6.17 kg/hm2 and 1.71 kg/hm2 respectively, which were nearly equal to those of HF. In conclusion, DF could significantly decreased runoff N and P loss, and was of great importance in protecting environment and controlling non-point pollution.