Wetlands sequestrate carbon at the highest rate than any other ecosystems on Earth. However, the spatial and temporal dynamics of GHGs emissions from the wetland ecosystems in China are still elusive. We synthesized 166 publications that contain 462 in situ measurements of GHGs emissions from the natural wetlands in China, and further analyzed the variability and the drivers of GHGs emissions in eight subdivisions of China's wetlands. The results show that the current studies are mainly concentrated in the estuaries, Sanjiang Plain, and Zoige wetlands. The average CO2 emissions, CH4 fluxes and N2O fluxes from Chinese wetlands were 218.84 mg·m−2·h−1, 1.95 mg·m−2·h−1 and 5.8 × 10−2 mg·m−2·h−1, respectively. The global warming potential (GWP) of China's wetlands was estimated to be 1881.36 TgCO2-eq·yr−1, with CO2 emissions contributing more than 65% to the GWP value. The combined GWP values of Qinghai-Tibet Plateau wetlands, coastal wetlands and northeastern wetlands account for 84.8% of GWP of China's wetlands. Correlation analysis showed that CO2 emissions increased with the increasing mean annual temperature, elevation, annual rainfall, and wetland water level, but decreased with soil pH. CH4 fluxes increased with the mean annual temperature and soil water content but decreased with the redox potential. This study analyzed the drivers of GHGs emissions from wetland ecosystems at the national scale, and GWP values of eight wetland subregions of China were comprehensively assessed. Our results are potentially useful for the global GHGs inventory, and can help assess the response of GHGs emissions of wetland ecosystem to environmental and climate change.