Ground cover rice production system is a promising technique with potentials to alleviate the effect of the increasing water-scarcity on rice production. Hence, finding appropriate management practices under this system is crucial for reducing global warming without yield loss. In this study, CH4 and N2O were quantified and contrasted in drip irrigation with plastic-film-mulch system (DP) and a continuous flooded rice cultivation system (CF) during two rice growing seasons of 2016 and 2017. The range of methane fluxes observed between irrigation regimes was (− 0.36 to 0.43 mg m−2 h−1) and (− 0.77 to 4.66 mg m−2 h−1) in 2016 and 2017 respectively. The cumulative CH4 emissions in 2017 under CF and DP were 16 times and 5 times higher than in 2016 respectively. DP reduced cumulative CH4 flux by 194% and 69% in 2016 and 2017 respectively compared to CF. Emissions of N2O were low and insignificant for both irrigation regimes. Grain yields were comparable between irrigation regimes with an insignificant reduction of 19% and 5% under DP in 2016 and 2017 respectively. The GWP of the 2-year average was 89% reduced under DP compared to CF. Our findings demonstrated that the DP mitigated GHGs while sustaining rice yield as a result of low nitrogen fertilization application and intermittent soil saturation level.