The subtropical region in Eastern China, with abundant hydrothermal resources and widely distributed lowland polders, is a traditional agricultural production area. The rice–wheat rotation system is often regarded as a dominant source of agricultural greenhouse gas (GHG) emissions. Under the general trend of global warming, it is of vital significance to explore farmland production methods for the reduction of GHGs. The study was based on a three-year field experiment conducted to investigate the effects of tillage methods (CF, conventional farming; OF, optimized fertilization; OF + N, optimized fertilization + no-tillage; OF + S, optimized fertilization + straw return) on the emissions of methane (CH₄) and nitrous oxide (N₂O) collected by way of “closed static box-gas chromatography”. The factors needing simultaneously monitored are atmospheric temperature, 5 cm ground temperature, soil redox potential (Eh), etc. Among the total Global warming potential (GWP) processed by CF, OF, OF + N, and OF + S, the GWP produced by CH₄ accounted for 86.01%, 88.23%, 86.34%, and 88.96%, respectively; The sequence of the total yields of rice and wheat is: OF > CF > OF + N > OF + S, the GWP is CF > OF + S > OF > OF + N, and that of greenhouse gas emission intensity (GHGI) is CF > OF + S > OF + N > OF. Comprehensively, tillage methods have great potential to reduce GWP, and OF is considered the optimal tillage method to achieve effective greenhouse gases reduction while ensuring stable and increased production.