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Based on landscape ecology, this study uses the mathematic models which reflect the landscape structure, dominance and heterogeneity, to build an eco-risk assessment method which can be applied in arid-oasis areas. Using the eco-risk assessment method and the field data measured in 2000 and 2011, we conduct a case study on the eco-risk assessment in the Hei River Basin, which is a typical arid-oasis ecosystem in China. Our results show that the total ecological risk value in the Hei River Basin has decreased from13.7 to 8.3 in the past 10 years and now the northern area is in greater risk than other areas. We can conclude that the eco-risk assessment method presented here can detect the spatial distribution and the time series change of the eco-risk in arid-oasis area. This method could assist environmental management decision making for arid-oasis ecosystem in the future.