Agricultural management practices (AMPs) have the potential to significantly enhance crop yield, albeit with the possible side effect of escalating greenhouse gas emissions. Few studies have undertaken a comprehensive quantification of the impact of AMPs on crop production and soil GHG, particularly in identifying the optimal AMPs for rice cultivation within rice-wheat rotation system. Here, we combined data analysis and keyword search methods on 1433 individual experimental observations from 172 studies on diverse soil types in the subtropical monsoon climate zone of China to assess the impact of AMPs on rice yield, CH4 and N2O emissions, total greenhouse gas emissions (TGHGE). We focused on four key AMPs: mineral N fertilizer management (including ordinary N fertilizer and slow−/controlled-release fertilizer (SCRF)), organic material management (incorporating organic fertilizer, biochar amendment, and straw return), water-saving irrigation, and no-tillage. Our result showed the rice yield ranged from 2525 to 31,196 kg ha−1, and mineral N fertilizer and organic material management boosted rice yield by 2.84–16.19 % and 2.47–8.52 %, respectively. In terms of N2O emissions, biochar amendment resulted in a decrease of 13.05 %, while ordinary N fertilizer, organic fertilizer, and water-saving irrigation led to increases of 63.16 %, 136.66 %, and 37.41 %, respectively. The implementation of SCRF, water-saving irrigation, and no-tillage significantly curtailed CH4 (6.83 %–35.91 %) and TGHGE (6.22 %–20.59 %). Conversely, organic fertilizer and straw return significantly escalated CH4 emissions by 102.20 % and 33.64 % and TGHGE by 85.03 % and 32.40 %. Rice yield and GHG emissions are mainly influenced by variables such as soil bulk density, pH, soil organic carbon, soil texture, mean annual temperature, and total nitrogen. Our study demonstrates that the application of SCRF, water-saving irrigation, and no-tillage can effectively reduce GHG without compromising yield. These practices are particularly effective under climatic and soil conditions of rice-wheat rotation systems in China, thereby contributing to the sustainable rice farming.