Research on selecting important terrestrial ecosystems for conservation is of strategic significance in improving China’s conservation efficiency and comprehensively planning China’s nature reserves systems. Using GIS analysis tools and five assessment criteria, China’s terrestrial ecosystems and their distribution areas for priority conservation are proposed based on the data of Vegetation in China, China’s Wetlands and Atlas of China’s vegetation. The criteria include “Dominant ecosystems in the eco-region", “Ecosystems with special climatic, geographic and soil features", “Ecosystems endemic to China", “Ecosystems with extremely rich species", and “Ecosystems with special habitats". Results indicate that China’s terrestrial ecosystems can be divided into 683 types, 135 of which are of high priority, including 75 forest ecosystems, 27 wetland ecosystems, 8 shrub ecosystems, 12 steppe ecosystems, 6 meadow ecosystems and 7 desert ecosystems. According to the distribution of priority ecosystems, 18 areas were selected as the center ones for the entire priority ecosystems. These areas should be considered primarily in the conservation of China’s terrestrial ecosystems. This research will contribute to configuration of China’s nature reserves and improve the effectiveness of China’s biodiversity conservation.