Soil-crop system plays an important role in the consumption of livestock manure, and the combination of organic manure and inorganic fertilizer is an important agricultural mode in increasing crop production, reducing the application of chemical fertilizer and protecting environment in the future. A pot experiment was conducted to study the effects of different dosages of inorganic nitrogen fertilizer on rice yield, nitrogen utilization and nitrogen loss risk in order to explore the optimal proportion of organic fertilizer and inorganic fertilizer and to provide scientific basis for the rational application of inorganic nitrogen when organic fertilizer used as base fertilizer in paddy fields. The results showed that when organic fertilizer used as base fertilizer in paddy fields, compared to the treatment of single organic fertilizer, crop yield, plant height, tillering number, nitrogen absorption by grains and nitrogen use efficiency all reached the highest when 0.8 times of inorganic nitrogen fertilizer was applied. With the increased application of inorganic nitrogen, nitrogen concentration in surface water of rice fields increased at the early stage of rice growth but decreased and then increased in the later stage of rice. Compared to the treatment of single organic fertilizer, nitrogen concentration in surface water significantly decreased by 17.5%, 11.9% and 9.3%, respectively under the treatments with 0.4, 0.6 and 0.8 times of conventional inorganic N application. Compared with the treatment with single nitrogen application, rice yield and nitrogen use efficiency were the highest under 0.8N+M treatment, and in which nitrogen concentration in surface water decreased by 29.9%. Therefore, based on the consumption of organic fertilizer and meet nitrogen demand of crops, 1:1 of organic nitrogen to inorganic nitrogen can not only increase rice yield, but also reduce nitrogen loss risk and the application rate of nitrogen fertilizer in paddy field.