Excess chemical fertilizer application results in substantial N2O emission. Manure application into agricultural soil can reduce chemical fertilizer input while maintaining crop yield. However, little is known about the potential effects of reduction in chemical fertilizer with green manure or organic manure on yield-scaled N2O emissions in orchards. A two-year experiment was carried out in a citrus orchard, including (i) chemical fertilizer (urea), 0%, 70%, 85% and 100% of N supplied, respectively (CK, C70, C85, CF), (ii) organic manure (rapeseed cake) incorporation with 0%, 70%, 85% and 100% of N supplied from chemical fertilizer (OM, OMC70, OMC85, OMCF), (iii) green manure (smooth vetch) incorporation with 0%, 70%, 85% and 100% of N supplied from chemical fertilizer (GM, GMC70, GMC85, GMCF) treatments. The soil physical-chemical properties, N2O emissions and yields were measured during 2018–2019. N2O emissions were 1.57 and 1.80 kg N ha−1 yr−1 under CF treatment in 2018 and 2019, respectively, and decreased by 25.4%−31.6% under C70, 32.5%−55.4% under OMC70 and OMC85 treatments and by 16.1–32.2% under GMC70 and GMC85 treatments. The 70% N rate of chemical fertilizer was the optimal N rate for maximizing yield in no manure, organic manure and green manure treatments, respectively. The C70, OMC70 and GMC70 treatments both significantly decreased yield-scaled N2O emission with the lowest emission in OMC70 treatment relative to CF treatment. N2O fluxes in OMC70 and OMC85 treatments were mainly controlled by the DOC/NO3- ratio, while soil NH4+ was the dominant factor controlling N2O fluxes in GMC70 and GMC85 treatments, suggesting that more NH4+ provided from green manure than from organic manure contributed to higher N2O emission. We conclude that applying organic manure incorporation with 30% reductions of chemical fertilizer is a fertilizer management strategy worth pursuing for sustainable productivity and environmental protection in citrus orchards.