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To evaluate the long-term effects of biochar amendment on greenhouse gas emissions (GHGs), a field experiment was conducted to examine the effects of 3-year field-aged biochar (B 3 ) and fresh biochar (B 0 ) on global warming potential (GWP) and greenhouse gas intensity (GHGI) of methane (CH 4 ) and nitrous oxide (N 2 O) in a typical rice-wheat rotation system. Four treatments were established as control without nitrogen fertilizer (CK), urea without biochar (N), urea with fresh biochar amended in 2015 (NB 0 ), and urea with 3-year field-aged biochar amended in 2012 (NB 3 ). Results showed that both the NB 0 and NB 3 treatments obviously increased soil pH, soil organic carbon (SOC), total nitrogen (TN) and influenced the potential activity of functional microorganisms related to GHGs compared to the N treatment. Relative to the N treatment, the NB 3 treatment significantly improved crop yield by 14.1% while reduced the CH 4 and N 2 O emissions by 9.0% and 34.0%, respectively. In addition, the NB 0 treatment significantly improved crop yield by 9.3%, while reduced the N 2 O emission by 38.6% though increased the CH 4 emissions by 4.7% relative to the N treatment. Moreover, both the NB 0 and NB 3 treatments could significantly reduce both GWP and GHGI, with NB 3 being more effective in simultaneously mitigating the GHGs emissions and enhancing crop yield. Since field-aged biochar showed obvious effects on GHGs mitigation and carbon sequestration after 3 years, biochar incorporations had long-term effect on GHGs mitigation and crop production in the rice-wheat rotation system.