Clinoptilolite zeolite (Z) has been widely used for reducing nutrient loss and improving crop productivity. However, the impacts of zeolite addition on CH4 and N2O emissions in rice fields under various irrigation regimes are still unclear. Therefore, a three-year field experiment using a split-plot design evaluated the effects of zeolite addition and irrigation regimes on greenhouse gas (GHG) emissions, grain yield, water productivity and net ecosystem economic profit (NEEP) in a paddy field. The field experiment included two irrigation regimes (CF: continuous flooding irrigation; AWD: alternate wetting and drying irrigation) as the main plots, and three zeolite additions (0, 5 and 10 t ha−1) as the subplots. The results indicated that AWD regime decreased seasonal cumulative CH4 emissions by 54%–71% while increasing seasonal cumulative N2O emissions by 14%–353% across the three years, compared with CF regime. Consequently, the yield-scaled global warming potential under AWD regime decreased by 10%–60% while grain yield, water productivity and NEEP improving by 4.9%–7.9%, 19%–27% and 12%–14%, respectively, related to CF regime. Furthermore, 5 t ha−1 zeolite addition mitigated seasonal cumulative CH4 emissions by an average of 36%, but did not significantly affect N2O emissions compared with non-zeolite treatment. In addition, zeolite addition at 5 and 10 t ha−1 significantly increased grain yield, water productivity and NEEP by 11%–21%, 13%–20% and 13%–24%, respectively, related to non-zeolite treatment across the three years. Therefore, zeolite addition at 5 t ha−1 coupled with AWD regime could be an eco-economic strategy to mitigate GHG emissions and water use while producing optimal grain yield with high NEEP in rice fields.