Reducing water input and promoting water productivity in rice field under alternate wetting and drying irrigation (AWD), instead of continuous flooding (CF), are vital due to increasing irrigation water scarcity. However, it is also important to understand how methane (CH4) and nitrous oxide (N2O) emissions and global warming potential ( of CH4 and N2O) respond to AWD under the influence of various factors. Here, we conducted a meta‐analysis to investigate the impact of AWD on CH4 and N2O emissions and , and its modification by climate conditions, soil properties, and management practices. Overall, compared to CF, AWD significantly reduced CH4 emissions by 51.6% and by 46.9%, while increased N2O emissions by 44.0%. The effect of AWD on CH4 emissions was significantly modified by soil drying level, the number of drying events, mean annual precipitation (MAP), soil organic carbon content (SOC), growth cycle, and nitrogen fertilizer (N) application. Regarding N2O emissions, mean annual temperature (MAT), elevation, soil texture, and soil pH had significant impacts on the AWD effect. Consequently, the under AWD was altered by soil drying level, soil pH, and growth cycle. Additionally, we found that MAP or MAT can be used to accurately assess the changes of global or national CH4 and N2O emissions under mild AWD. Moreover, increasing SOC, but not N application, is a potential strategy to further reduce CH4 emissions under (mild) AWD, since no difference was found between application of 60–120 and > 120 kg N ha−1. Furthermore, the soil pH can serve as an indicator to assess the reduction of under (mild) AWD as indicated by a significant linear correlation between them. These findings can provide valuable data support for accurate evaluation of non‐CO2 greenhouse gas emissions reduction in rice fields under large‐scale promotion of AWD in the future.