Sources of methane (CH4) become highly variable for countries undergoing a heightened period of development due to both human activity and climate change. An urgent need therefore exists to budget key sources of CH4, such as wetlands (rice paddies and natural wetlands) and lakes (including reservoirs and ponds), which are sensitive to these changes. For this study, references in relation to CH4 emissions from rice paddies, natural wetlands, and lakes in China were first reviewed and then reestimated based on the review itself. Total emissions from the three CH4 sources were 11.25 Tg CH4 yr−1 (ranging from 7.98 to 15.16 Tg CH4 yr−1). Among the emissions, 8.11 Tg CH4 yr−1 (ranging from 5.20 to 11.36 Tg CH4 yr−1) derived from rice paddies, 2.69 Tg CH4 yr−1 (ranging from 2.46 to 3.20 Tg CH4 yr−1) from natural wetlands, and 0.46 Tg CH4 yr−1 (ranging from 0.33 to 0.59 Tg CH4 yr−1) from lakes (including reservoirs and ponds). Plentiful water and warm conditions, as well as its large rice paddy area make rice paddies in southeastern China the greatest overall source of CH4, accounting for approximately 55% of total paddy emissions. Natural wetland estimates were slightly higher than the other estimates owing to the higher CH4 emissions recorded within Qinghai-Tibetan Plateau peatlands. Total CH4 emissions from lakes were estimated for the first time by this study, with three quarters from the littoral zone and one quarter from lake surfaces. Rice paddies, natural wetlands, and lakes are not constant sources of CH4, but decreasing ones influenced by anthropogenic activity and climate change. A new progress-based model used in conjunction with more observations through model-data fusion approach could help obtain better estimates and insights with regard to CH4 emissions deriving from wetlands and lakes in China.