The Mekong Delta paddies are known as hotspots of methane emission, but these emissions are not well studied. We analyzed methane emission patterns based on monitoring data from typical triple rice cropping paddies collected over 5 years. We found that the total emissions in a crop season doubled in the second crop, tripled in the third crop, and reset after the annual natural flood of the Mekong River. The emission peaks occurred around 0 to 3 weeks after starting irrigation, then gradually decreased. This suggests that methane was generated by the soil organic matter, because the small rice plants provide little carbon for methanogenesis. In general, the main source of emitted methane is rice-derived carbon by current-season photosynthates and the emission peaks at the rice heading stage. However, the contribution of the rice-derived carbon is negligible in the hotspot paddies while total emission is high. The increase in emission levels from the first to the third crop can be explained by the accumulation of rice residue from the preceding crops, especially rice straw incorporated into the soil. The reset of emission levels after annual flood means that the rice straw is decomposed without methanogenesis in water with dissolved oxygen. Thus, the annual emission pattern shows that decomposing rice straw in paddy surface-water is an effective method to reduce methane emissions.