Rice paddies account for approximately 9% of human-induced methane (CH4) emissions. Nitrogen (N) fertilization affects CH4 emissions from paddy soils through several conflicting mechanisms, but the quantitative importance of these N effects and their primary drivers are still unclear, causing large uncertainty in global CH4 projections and mitigation options. Here we show that the impacts of N fertilizers on CH4 emissions from rice paddies can be largely predicted by soil pH. Specifically, N fertilization stimulates CH4 emissions most strongly in acidic soils by accelerating organic matter decomposition and increasing the activities of methanogens. Accounting for the interactions between soil pH and N fertilization, we estimate that N fertilization has raised the total CH4 emission from rice paddies by 52% (+8.0 Tg yr-1) globally.