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Few studies have investigated ecosystem risk under climate change from the perspective of critical thresholds. We presented a framework to assess the climate change risk on ecosystems based on the definition of critical thresholds. Combined with climate scenario, vegetation, and soil data, the Atmosphere Vegetation Interaction Model version 2 was used to simulate net primary productivity in the period of 1961-2080. The thresholds of dangerous and unacceptable impacts were then defined, and climate change risks on ecosystems in China were assessed. Results showed that risk areas will be closely associated with future climate change and will mainly occur in the southwest and northwest areas, Inner Mongolia, the southern part of the northeast areas, and South China. The risk regions will expand to 343.66Mha in the long term (2051-2080), accounting for 35.80% of China. The risk levels on all ecosystems (eco-regions) are likely to increase continually. The ecosystems of wooded savanna, temperate grassland, and desert grassland, which typically exhibit strong water stress, will have the maximum risk indices in the future. The Northwest Region is likely to be the most vulnerable because of precipitation restrictions and obvious warming. By contrast, Qinghai-Tibet Region will not be so vulnerable to future climate change.