Green manure is a widely applied to increase grain yield, while it also attributes to greenhouse gas (GHG) emissions in agriculture ecosystems. Combining green manure with inorganic fertilizer inputs is a common practice that can influence soil GHG emissions and grain yield, however, its impacts on grain yield and global warming potential (GWP) under different initial soil conditions before rotating experiments and agronomic management in paddy fields remain unclear. We synthesized 508 data pairs to evaluate the responses of CO2 emissions, CH4 emissions, N2O emissions, and grain yield to combined inputs of green manure plus inorganic fertilizer compared with only inorganic fertilizer application. Our findings indicate that both inorganic fertilizer plus extra green manure (GM-E) and green manure substitutes for inorganic fertilizer (GM-S) could increase CO2 emissions (22.5 %−76.8 %), CH4 emissions (100 %−103 %), N2O emissions (29.8 %−50.9 %), and yield (2.21 %−19.6 %). Except for GM-E, which showed a non-significant increase in grain yield. The initial soil properties before rotating experiments, the types and timing of green manure application were key drivers of GHG emissions and yield, and extra green manure applied in areas with low initial soil pH and high C:N can increase GWP and yield. Overall, the mixed green manure application had greater impact than leguminous or non-leguminous green manure applied alone. The responses of GHG emissions and yield to GM-S were modulated by mean annual precipitation and initial soil properties before rotating experiments, and green manure substitutes for inorganic fertilizer in areas with high initial soil pH and low C:N can increase GWP and yield. Meanwhile, excessive precipitation caused a reduction in yield and a significant increase in GWP intensity. Our results showed that extra green manure applications of less than 68.1 kg N ha−1 would not significantly increase GWP. Therefore, an effective green manure strategy can achieve a win-win situation for the dual challenge of agricultural production and climate change mitigation.