Straw incorporation promotes rice productivity and soil fertility. However, the effects of tillage practice with straw on GHG emissions in paddy fields are not well documented. Under three rice-based cropping systems of China (single rice, double rice and rice-wheat cropping systems), we investigated rice yield, CH4, N2O, area and yield-scaled emissions arising from different straw-incorporated tillage patterns. Tillage with straw affected rice yield by −6.8~3.2%, −9.1~9.0% and −9.8~2.1% in single rice, rice-wheat and double rice cropping systems respectively. Straw impacted CH4 emission but tillage influenced its impact irrespective of the rice cropping system. The highest CH4 emissions occurred in RedT + S, RoT + S and RoT + S under single rice, rice-wheat and double rice cropping systems respectively. Cumulative CH4 emission of PT + S decreased by 46.8% (p 4 emission of PT + S decreased by 19.0% (p p > 0.05) respectively compared with RoT + S. Lower methanogenic abundance of PT + S translated into the lowest cumulative CH4, area and yield scaled emissions in single rice and double rice cropping systems. To maintain high rice yield and reduce GHG emissions from straw incorporation, PT + S is recommended for a rice-based cropping system.