The ecosystem based protection, an effective way to prevent the loss of biodiversity, is a hot topic in the field of conservation biology. As resources are always inadequate to monitor all components of biodiversity, criteria must be applied to prioritize both species and ecosystem for conservation and management plan. While there are many methods for prioritizing species, criteria for prioritizing ecosystem are not well developed. To provide the basis for the development of ecosystem protection plan, International Conservation Organization and researchers have been dedicated to working over the ecosystem conservation priority by developing quantitative criteria and methods for local, regional and global level ecosystem protection. The first step for assessing ecosystem conservation priority is properly defined and classified ecosystem as unit of analysis. Then, we select criteria and methods that the conservation priority can be assessed quantitatively. Finally, based on the above outcomes, the ecosystem conservation priority can be ranked in low, medium, and high priority. The criteria used for assessment are grouped into three classes: ecosystem area loss rate, ecosystem extent (area), and ecosystem representativeness. In this paper, we take ecosystems in Jiangxi Province as a case to show the process for ecosystem conservation priority assessment. We explain the use of these criteria for assessing ecosystem conservation priority, the vegetation digital map in 1980s, land-use map in 2010 and national nature reserves map are used to evaluate the ecosystem conservation priority by overlying, reclassing, normalizing and quantitative assessing in GIS. The conservation priority of nature ecosystems in Jiangxi Province is ranked in low, moderate and high level, respectively. The result shows that a total area of nature ecosystems reduced by 82613.83km² which account more than 60% of its area. There are 19 ecosystem types among the total 37 ecosystem types in Jiangxi province have been protected by National Nature Reserves, but the ratio of protection area for each of these ecosystems is still low. The ratio to the total area of Jiangxi Province for forest ecosystems ranking in high, moderate and low priority is 16.7374%, 5.5310%, and 3.8242%; the ratio for shrub ecosystems is 0.0975%, 0.9335%, and 0.0100%; the ratio for grassland ecosystems is 0.2647%, 0.0005%, and 0.1064%; and the ratio for wetland ecosystems is 0.3532%, 0.1127%,and 1.5650%, respectively. The ratio of protected area by national nature reserves for forest ecosystems ranking in high, moderate, and low priority level is 0.51%, 3.73%, and 5.76%; the ratio for shrub ecosystems is 1.72%, 0.17%, and 0.70%; the ratio for grassland ecosystems is 0.21%, 0.00%, and 3.49%; and the ratio for wetland ecosystems is 1.87%, 0.00%, and 18.01%, respectively. The spatial pattern for the ecosystems in different conservation priority level shows that the ecosystems in high conservation priority ranking are mainly distributed in the south-east and north-west part, the ecosystems in moderate conservation priority ranking are mainly distributed in north-east and north-west part, and the ecosystems in low conservation priority ranking are mainly distributed in the north part. Due to the economic growth and social development in the past 30 years, most of the ecosytem types which distributed in the central part of Jianxi province are changed to agricultural and city ecosystems. Combined with the present status of the nature ecosystems in Jiangxi province, the ecosystems ranking in high conservation priority which account for 17.46% of the total area of Jiangxi province are suggested to protect first. These results have practical value for ecosystem level conservation, especially in the ecosystem conservation planning.