Natural wetlands are thought to be one of the largest natural sources of atmospheric methane concentrations. Although numerous studies referred to the rate of methane fluxes in different geophysical regions, only a few had estimates of the overall geographical methane emissions in China. This study estimated the spatial variations of annual methane emissions with the pixel size of 1 km × 1 km from natural wetlands, excluding water surface, in China. The natural wetland areas were extracted from the database of the 2000 land covers, and geophysical divisions were used to represent different climate conditions. Methane emission in every geophysical region was calculated based on methane release factors obtained from an extensive review of published literature, as well as the data of elevation and vegetation proportion in the region. The estimated annual methane emissions ranged from 0 to 5702.8 kg per pixel within the area of 1 km2, and the spatial variation of methane emissions was strongly correlated with proportion of wetlands in the area. The total methane emission from natural wetlands in China ranged from 3.48 to 7.16 Tg (terrogram, unit of weight) CH4 per year, with the mean value of 4.94 Tg CH4 per year, based on an area of 133,000 km2 of natural wetlands. Specifically, the wetlands in northeast China had the highest contribution in China (39%). Inner Mongolia and Qinghai-Tibet highlands represented about 25% and 21%, respectively. The other 15% of the measured methane was released in northwest, north, central, and south China.