Freshwaters are important sources of greenhouse gases (GHGs) to the atmosphere that may partially offset the terrestrial carbon sink. However, current emission estimates from inland waters remain uncertain due to data paucity in key regions with a large freshwater surface area, such as China. Here, we show that the areal fluxes of GHGs (carbon dioxide, methane, and nitrous oxide) from lakes and reservoirs in China are much larger than previous estimates. Our work summarized data from 310 lakes and 153 reservoirs, and revealed diffusive emissions of 1.56 (95% confidence interval: 1.12–2.00) Tg C-CH4/y and 25.2 (20.8–29.5) Tg C-CO2/y from reservoirs and lakes. Chinese lakes and reservoirs emit 175.0 (134.7–215.3) Tg CO2 equivalent, with 73.4% of this forcing contributed by lakes. These aquatic sources are equivalent to 14.1%–22.6% of China's estimated terrestrial carbon sink. Our results suggest a disproportionally high contribution of China's reservoirs and lakes to national and global GHGs emissions, highlighting major data gaps and the need of including more artificial and natural lakes data from developing countries like China in global GHGs budgets.