Ecology is playing a core role in ecosystem management and in sustainable development of the life support system. Quantitative study of the ecosystem is crucial in ecosystem management and is becoming the research frontier. In this study, new method for measuring ecosystem risk is established by combining capitalization of natural asserts and financial risk method. Some models to calculate the total ecosystem risk for a region or watershed are established. A case study of the method is conducted in Minqin oasis ecosystem. The case study shows how to calculate the risk value of an ecosystem. The result of the case study indicates that the maximum loss of the region′s ecosystem value is no more than 192 million RMB yuan at 95% confidential level in three years. The method and formulae established for ecosystem risk analysis are useful in ecosystem management.