The optimization of fertilization management has the potential to improve crop yield, reduce greenhouse gas (GHG) emissions and enhance nitrogen agronomy efficiency (NAE). However, less is known about whether these benefits can be simultaneously achieved by optimizing fertilization regimes in Chinese croplands. We carried out a year-round field experiment to measure methane (CH4) and nitrous oxide (N2O) fluxes, crop yield and NAE under different fertilization regimes in a subtropical double-rice cropping system. Relative to the conventional chemical N fertilizer application (F), alternative fertilization strategies significantly decreased N2O emissions by 26–78% when averaged across the options of chemical N fertilizer application with reduced rates (RF, 30% off), chemical N fertilizer fully replaced by organic N fertilizer with reduced rates (OF, 30% off) and chemical N fertilizer fully replaced by controlled-release N fertilizer with reduced rates (CF, 30% off), with the largest mitigation potential occurring in OF-treated plots, but comparable extents between the early- and late-rice seasons. Soil CH4 emissions had no consistent response to alternative fertilization regimes, showing contrasting seasonal patterns between in the early- and late-rice seasons. Alternative fertilization options consistently increased NAE by 7–36% and 30–38% in the early- and late-rice seasons, respectively, and this benefit was maximized in OF-treated plots. Direct emission factors of N fertilizer for N2O and the combined greenhouse gas intensity (GHGI) of N2O and CH4 were negatively related to NAE while rice yield was positively related to NAE. Our findings suggest that optimized fertilization strategies especially through the option of chemical N fertilizer fully substituted by organic N fertilizer can reconcile low climatic impact and high NAE, but without compromising yield in double-rice cropping systems.