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Abstract: Annual paddy rice–winter wheat rotation constitutes one of the typical cropping systems in southeast China, in which various water regimes are currently practiced during the rice-growing season, including continuous flooding (F), flooding-midseason drainage-reflooding (F-D-F), and flooding-midseason drainage-reflooding and moisture but without waterlogging (F-D-F-M). We conducted a field experiment in a rice–winter wheat rotation system to gain an insight into the water regime-specific emission factors and background emissions of nitrous oxide (N2O) over the whole annual cycle. While flooding led to an unpronounced N2O emission during the rice-growing season, it incurred substantial N2O emission during the following non-rice season. During the non-rice season, N2O fluxes were, on average, 2.61 and 2.48mg N2O–Nm− 2 day−1 for the 250kg N ha−1 applied plots preceded by the F and F-D-F water regimes, which are 56% and 49% higher than those by the F-D-F-M water regime, respectively. For the annual rotation system experienced by continuous flooding during the rice-growing season, the relationship between N2O emission and nitrogen input predicted the emission factor and background emission of N2O to be 0.87% and 1.77kg N2O–Nha−1, respectively. For the plots experienced by the water regimes of F-D-F and F-D-F-M, the emission factors of N2O averaged 0.97% and 0.85%, with background N2O emissions of 2.00kg N2O–Nha−1 and 1.61kg N2O–Nha−1 for the annual rotation system, respectively. Annual direct N2O–N emission was estimated to be 98.1Gg yr−1 in Chinese rice-based cropping systems in the 1990s, consisting of 32.3Gg during the rice-growing season and 65.8Gg during the non-rice season, which accounts for 25–35% of the annual total emission from croplands in China. [Copyright &y& Elsevier]