Abstract. Natural wetlands are among the most important sources of methane; thus, these areas are important for better understanding long-term temporal variations in atmospheric methane concentration. During the last 60 years, wetlands have experienced extensive conversion and global impacts from climate warming, which makes the estimation of methane emission from wetlands highly uncertain. In this paper, we present a modeling framework, integrating CH4MODwetland, TOPMODEL and TEM models, to analyze the temporal and spatial variations in CH4 emissions from natural wetlands (including inland wetlands, coastal wetlands, lakes and rivers) in China. Our analysis revealed an increase of 25.5%, averaging 0.52 g m−2 per decade, in national CH4 fluxes from 1950 to 2010, which was mainly induced by climate warming. Higher rates of increasing CH4 fluxes occurred in northeastern, northern and northwestern China, associated with large temperature increases. However, decreases in precipitation due to climate warming offset the increase in CH4 fluxes in these regions. The CH4 fluxes from the wetland on the Qinghai Tibetan Plateau exhibited a lower rate of increase, which was approximately 25% of that simulated in northeastern China. Although climate warming has accelerated CH4 fluxes, the total amount of national CH4 emissions decreased by approximately 2.35 Tg (1.91–2.81 Tg), i.e., from 4.50 Tg in the early 1950s to 2.15 Tg in the late 2000s, due to a large wetland loss of 17.0 million ha. Of this reduction, 0.26 Tg (0.24–0.28 Tg) was derived from lakes and rivers, 0.16 Tg (0.13–0.20 Tg) from coastal wetlands, and 1.92 Tg (1.54–2.33 Tg) from inland wetlands. Northeastern China had the largest contribution to this reduction, with a loss of 1.68 Tg. The CH4 emissions were reduced by more than half in most regions in China except for the Qinghai Tibetan Plateau, where only a 23.3% decrease in CH4 was observed.