To investigate the spatial and seasonal variations of nitrous oxide (N2O) fluxes and understand the key controlling factors, we explored N2O fluxes and environmental variables in high marsh (HM), middle marsh (MM), low marsh (LM), and mudflat (MF) in the Yellow River estuary throughout a year. Fluxes of N2O differed significantly between sampling periods as well as between sampling positions. During all times of day and the seasons measured, N2O fluxes ranged from -0.0051 to 0.0805 mg N2O m(-2) h(-1), and high N2O emissions occurred during spring (0.0278 mg N2O m(-2) h(-1)) and winter (0.0139 mg N2O m(-2) h(-1)) while low fluxes were observed during summer (0.0065 mg N2O m(-2) h(-1)) and autumn (0.0060 mg N2O m(-2) h(-1)). The annual average N2O flux from the intertidal zone was 0.0117 mg N2O m(-2) h(-1), and the cumulative N2O emission throughout a year was 113.03 mg N2O m(-2), indicating that coastal marsh acted as N2O source. Over all seasons, N2O fluxes from the four marshes were significantly different (p < 0.05), in the order of HM (0.0256 ± 0.0040 mg N2O m(-2) h(-1)) > MF (0.0107 ± 0.0027 mg N2O m(-2) h(-1)) > LM (0.0073 ± 0.0020 mg N2O m(-2) h(-1)) > MM (0.0026 ± 0.0011 mg N2O m(-2) h(-1)). Temporal variations of N2O emissions were related to the vegetations (Suaeda salsa, Phragmites australis, and Tamarix chinensis) and the limited C and mineral N in soils during summer and autumn and the frequent freeze/thaw cycles in soils during spring and winter, while spatial variations were mainly affected by tidal fluctuation and plant composition at spatial scale. This study indicated the importance of seasonal N2O contributions (particularly during non-growing season) to the estimation of local N2O inventory, and highlighted both the large spatial variation of N2O fluxes across the coastal marsh (CV = 158.31%) and the potential effect of exogenous nitrogen loading to the Yellow River estuary on N2O emission should be considered before the annual or local N2O inventory was evaluated accurately.