Quantifying greenhouse gas intensity (GHGI) and soil carbon sequestration is a method to assess the mitigation potential of agricultural activities. However, the effects of different fertilizer amendments on soil carbon sequestration and net GHGI in a rice-wheat cropping system are poorly understood. Here, fertilizer treatments including PK (P and K fertilizers); NPK (N, P and K fertilizers), NPK + OM (NPK plus manure), NPK + SR (NPK plus straw returning), and NPK + CR (NPK plus controlled-release fertilizer) with equal N input were conducted to gain insight into the change of soil organic carbon (SOC) derived from the net ecosystem carbon budget (NECB), net global warming potential (GWP), and GHGI under rice-wheat rotation. Results showed that compared with NPK treatment, NPK + OM significantly increased wheat yield and NPK + SR caused significant increase in rice yield. Meanwhile, NPK + SR and NPK + CR treatments reduced net GWP by 30.80% and 21.83%, GHGI by 36.84% and 28.07%, respectively, which suggested that improved grain production could be achieved without sacrificing the environment. With the greatest C sequestration, lowest GHGI, the NPK plus straw returning practices (NPK + SR) might be the best strategy to mitigate net GWP and improve grain yield and NUE in the current rice-wheat rotation system.