Increasing reactive nitrogen (N) input has been recognized as one of the important factors influencing climate system through affecting the uptake and emission of greenhouse gases (GHG). However, the magnitude and spatiotemporal variations of N-induced GHG fluxes at regional and global scales remain far from certain. Here we selected China as an example, and used a coupled biogeochemical model in conjunction with spatially explicit data sets (including climate, atmospheric CO2, O3, N deposition, land use, and land cover changes, and N fertilizer application) to simulate the concurrent impacts of increasing atmospheric and fertilized N inputs on balance of three major GHGs (CO2, CH4, and N2O). Our simulations showed that these two N enrichment sources in China decreased global warming potential (GWP) through stimulating CO2 sink and suppressing CH4 emission. However, direct N2O emission was estimated to offset 39% of N-induced carbon (C) benefit, with a net GWP of three GHGs averaging −376.3 ± 146.4 Tg CO2 eq yr−1 (the standard deviation is interannual variability of GWP) during 2000–2008. The chemical N fertilizer uses were estimated to increase GWP by 45.6 ± 34.3 Tg CO2 eq yr−1 in the same period, and C sink was offset by 136%. The largest C sink offset ratio due to increasing N input was found in Southeast and Central mainland of China, where rapid industrial development and intensively managed crop system are located. Although exposed to the rapidly increasing N deposition, most of the natural vegetation covers were still showing decreasing GWP. However, due to extensive overuse of N fertilizer, China's cropland was found to show the least negative GWP, or even positive GWP in recent decade. From both scientific and policy perspectives, it is essential to incorporate multiple GHGs into a coupled biogeochemical framework for fully assessing N impacts on climate changes.