Abstract: Lakes are key components of the Earth’s Critical Zone and significant parts of the water cycle, matter cycles and energy cycles. In order to comprehend the lake distribution in China, based on the “Eco-geological Survey Project” of China Geological Survey and its sub-project “National Remote Sensing Geological Survey of Earth’s Critical Zones”, the authors in this research used Landsat8 OLI satellite images, remote sensing interpretation and other technical methods to identify 2 780 lakes(lake area≥1.0 km²) with a total area of 78 727.9 km² in the territory of China (not including Hong Kong, Macao and Taiwan areas). The number, area and distribution characteristics of lakes in China’s provincial-level administrative regions, five typical lake regions, and the main river basins are analyzed. In addition, the research aims at the ecological problems in typical lake regions, and relevant suggestions on lake ecological protection and restoration are put forward. The lakes in the northern agro-pastoral ecotone have shrunk and dried up, mainly due to the development of agriculture and animal husbandry and serious groundwater over-exploitation, so efforts should be made to reduce groundwater exploitation. The disorderly development and excessive pursuit of landscape water surface expansion exists in the construction of artificial lakes in the Yellow River Basin, so we should follow the natural law of water cycle and water balance and regulate the allocation of water resources in the whole basin. The water surface of lakes in the source area of the Yangtze River is in an expanding state as a whole, mainly due to natural factors and supplemently by human activities. The monitoring of frozen soil change process and water ecology and water environment of main rivers should be strengthened to comprehensively improve the overall monitoring level of the source area. The research results provide a method reference for the follow-up ecological protection and restoration work.