Abstract China’s rice agriculture, a primary source of greenhouse gases (GHGs), has experienced great changes in the last five decades due to changes in dominant varieties and farming practices. However, the impacts of these changes on GHG emissions have not been comprehensively assessed. While most earlier studies focused on the GHG emissions per unit area, recent research indicated that the yield-scaled impact may better reflect the reality. Through integrating the results from a meta-analysis, two multi-site field experiments and an expert survey, we quantify the integrated impacts of different practices on both area- and yield-scaled GHG emissions in China. Results from the expert survey showed that rice planting area has shifted northwards, and alternate water-saving (WS) irrigation has been applied in nearly 78% of Chinese rice paddy areas in both the rice nursery stage and post-transplanting period over the past five decades. The changes of these practices and replacement of new rice varieties have increased China’s rice yield by 131%. During the same period, cropping system adjustment, variety replacement, and implementation of WS irrigation have reduced total GHG emissions by 7%, 31%, and 42%, respectively. Also, the major decrease in GWP occurred prior to the 2000s, and the decreasing trend continued in the post-2000s period but at a slower rate. Our results have some limitations as these estimates ignore a number of important variations and interactions among management factors as well as climatic and edaphic conditions. Still, our findings illustrate that it is possible to enhance rice productivity at reduced environmental costs through screening for low emission varieties and agronomic practices. Future innovations should ensure that rice farming progressively adapts to climate change, while continuing to reduce GHG emissions.