CH4 is the second largest contributor to human‐induced global warming. However, large uncertainties still exist regarding the magnitude and temporal variation of CH4 exchanges in China's natural ecosystems, especially under climate changes. In this study, we assessed its uncertainty and temporal variation during 1979–2012, by integrating a biogeochemical model, extensive in situ measurements, and various sources of wetland maps. Uncertainty analyses suggested that previous studies might have underestimated CH4 emissions, primarily due to bias in wetland extents in NE China. After that, 1 km resolution wetland maps were used to drive the model, together with a 0.1° resolution climate data set. The model showed that China's natural wetlands emitted 4.56 ± 1.24 Tg CH4 yr−1 during the 1980s, which decreased to 3.86 ± 1.09 Tg CH4 yr−1 in the 2000s, mainly due to wetland drainage in NE China. However, recent glacier‐melt‐induced wetland expansion has enhanced CH4 emissions by 28% on the Tibetan Plateau since the 1980s. The magnitude of CH4 uptake by the natural ecosystems has remained relatively stable, e.g., −2.57 ± 0.18 and −2.70 ± 0.19 Tg CH4 yr−1 in the 1980s and 2000s, respectively. In summary, the net CH4 balance of China's natural ecosystems has shown a decreasing pattern, i.e., 1.99 ± 1.42 and 1.16 ± 1.28 Tg CH4 yr−1 in the 1980s and 2000s, respectively, despite distinct regional differences between NE China and the Tibetan Plateau. Furthermore, this study emphasizes the correct representation of wetland extent and its dynamics, i.e., wetland drainage in populated regions and wetland expansion in glacier‐fed regions, in driving the decadal CH4 exchange magnitude.