Mitigating greenhouse gas (GHG) emissions from irrigated rice while maintaining productivity remains a major challenge in sustainable water management. This study aimed to identify an optimized irrigation regime within the System of Rice Intensification (SRI) by reducing greenhouse gas emission and maintain grain yield as well as increasing water-use efficiency (WUE) across three crop seasons in Bogor, Indonesia. Three irrigation regimes were applied with different water levels, i.e., Flooded with water depth in between 2-5 cm (FL), WET with 0 - 1 cm water depth, and DRY with -5 cm below the soil surface. Methane (CH4) and nitrous oxide (N2O) fluxes were measured weekly using a closed chamber method, and seasonal GWP was calculated to assess total GHG emissions. As results, a clear trade-off between CH4 and N2O emissions in total was observed across regimes due to differences in water status. The DRY regime significantly reduced CH4 emissions and has the lowest overall GWP, which was approximately 28% lower than the WET regime and 39% lower than the FL regime. Although the DRY regime released N2O emissions slightly higher than the FL regime, it has significantly lower impact on climate due to the reduction in CH4 emissions. Among the regimes, grain yield was not differed significantly, with mean yields ranging from 6.05 to 6.39 t ha⁻¹ across the seasons. Moreover, the DRY regime was saving more irrigation water and gained the highest water-use efficiency, by 31 - 53% in the first season and 11 - 29% in the third season. These demonstrate that controlled water levels under the DRY scenario within SRI systems can simultaneously maintain rice productivity, enhance water-use efficiency, and reduce GHG emissions.