Organic fertilizer can improve soil structure and enhance the nutrient content in soil and is beneficial to sustainable agricultural development. However, the influence of organic fertilizer substitutions on NH and NO emissions from farmland is unclear. Thus, we set up an organic substitution field experiment in Northeast China. The experiment included six treatments: single application of chemical fertilizers (NPK: 250 kg N ha); NO, 10% reduction in chemical nitrogen fertilizers (225 kg N ha) + chicken manure (25 kg N ha); NO, 20% reduction in chemical nitrogen fertilizers (200 kg N ha) + chicken manure (50 kg N ha); NO, 30% reduction in chemical nitrogen fertilizers (175 kg N ha) + chicken manure (75 kg N ha); NO, 40% reduction in chemical nitrogen fertilizers (150 kg N ha) + chicken manure (100 kg N ha); and no-nitrogen fertilizer (CK). This experiment investigated the effects of partial substitution of chemical nitrogen fertilizer with organic fertilizer on NH and NO emissions and nitrogen use efficiency in a maize field. The results showed that, compared with chemical N, organic fertilizer mitigated NH volatilization but promoted the soil NO total emissions during the whole growth stage. NH cumulative volatilization decreased with the increase in the substitution rate of organic fertilizer. Compared with the NPK treatment, the cumulative volatilization of NH in the NO and NO treatments decreased by 15.24 and 17.92%, respectively. The NO treatment had the highest NO emission in the whole growth stage, and the NO emission of the NO treatment increased by 10.72% compared to the NPK treatment. Moreover, the yield, partial factor productivity (PFP), nitrogen harvest index (NHI), and apparent nitrogen recovery efficiency (NRE) of NO treatment were the highest of all treatments, and the yields, PFP, plant N accumulation, grain N accumulation, and the cumulative emissions of NH and NO were similar to N treatment. In conclusion, nitrogen fertilizer use efficiency was enhanced, decreasing environmental pollution from livestock under organic fertilizer substitution conditions. We suggested 20% or 30% substitution rates of organic fertilizer were proper.