N distribution in soil-plant system and N2O emissions from soil was investigated in a long-term fertilization field experiment in fluvo-aquci soil in North China. In this experiment, there were 7 treatments: organic manure N (OM), half organic manure N and half fertilizer N (1/2OM), fertilizer NPK (NPK), fertilizer NP (NP), fertilizer NK (NK), fertilizer PK (PK) and control (CK). The results showed that N2O emissions from soil during maize growth was higher than during wheat growth, but the differences of soil N2O emissions among the treatments were insignificant in same N fertilization. Balanced fertilization of N, P and K increased soil N storage, while the efficiency of organic manure N application was higher than chemical N application. N utilization efficiency and distribution in plants was also significantly influenced by the fertilization. Balanced nutrient application was beneficial to N accumulation in seeds, but nutrient deficiency was inclined to accumulate N in straws. The N lost from soil was highest in NK and least in 1/2OM treatment. In summary, application of P fertilizer and organic manure not only reduce the indirect N2O emission from soil, but also increase soil fertility and crop yields.