The impact of agricultural management on global warming potential (GWP) and greenhouse gas intensity (GHGI) is not well documented. A long-term fertilizer experiment in Chinese double rice-cropping systems initiated in 1990 was used in this study to gain an insight into a complete greenhouse gas accounting of GWP and GHGI. The six fertilizer treatments included inorganic fertilizer [nitrogen and phosphorus fertilizer (NP), nitrogen and potassium fertilizer (NK), and balanced inorganic fertilizer (NPK)], combined inorganic/organic fertilizers at full and reduced rate (FOM and ROM), and no fertilizer application as a control. Methane (CH4) and nitrous oxide (N2O) fluxes were measured using static chamber method from November 2006 through October 2009, and the net ecosystem carbon balance was estimated by the changes in topsoil (0–20 cm) organic carbon (SOC) density over the 10-year period 1999–2009. Long-term fertilizer application significantly increased grain yields, except for no difference between the NK and control plots. Annual topsoil SOC sequestration rate was estimated to be 0.96 t C ha−1 yr−1 for the control and 1.01–1.43 t C ha−1 yr−1 for the fertilizer plots. Long-term inorganic fertilizer application tended to increase CH4 emissions during the flooded rice season and significantly increased N2O emissions from drained soils during the nonrice season. Annual mean CH4 emissions ranged from 621 kg CH4 ha−1 for the control to 1175 kg CH4 ha−1 for the FOM plots, 63–83% of which derived from the late-rice season. Annual N2O emission averaged 1.15–4.11 kg N2O–N ha−1 in the double rice-cropping systems. Compared with the control, inorganic fertilizer application slightly increased the net annual GWPs, while they were remarkably increased by combined inorganic/organic fertilizer application. The GHGI was lowest for the NP and NPK plots and highest for the FOM and ROM plots. The results of this study suggest that agricultural economic viability and GHGs mitigation can be simultaneously achieved by balanced fertilizer application.