The impact of long-term fertilizer application on greenhouse gas emission and global warming potential (GWP) is not well documented. A long-term fertilizer experiment, located at the Hailun State Key Agro-ecological Experiment Station, Hailun County, Heilongjiang Province, China, was used in this study to completely account for emission of CO 2 and N 2O from maize-soybean rotation systems. Five treatments were implemented, including nitrogen and potassium (NK), nitrogen and phosphorus (NP), balanced inorganic fertilizer (NPK), combined inorganic/organic fertilizer (NPKM), and no fertilizer (Cont.). CO 2 and N 2O fluxes were measured using a closed-chamber method from May 2006 to April 2007, and net GWP was estimated using emission data and considering CO 2 fixed by crops. With the exception of NK in soybean, long-term fertilizer application significantly increased crop biomass in all treatments and both crops compared to Cont. plots. Long-term inorganic fertilizer application tended to decrease total CO 2 emission and increase total N 2O emission. Inorganic/organic combination fertilizer significantly increased CO 2 and N 2O emission by 41% and 388% compared to the Cont., respectively. Compared with the Cont., inorganic fertilizer application significantly decreased total net GWP by 179%; in contrast, net GWP was increased 82% by inorganic/organic combination fertilizer application. The results of this study indicate that reduction of GWP and agricultural economic gain can be simultaneously achieved by appropriate fertilizer application.