Assessment of vulnerability for natural ecosystem to climate change is a hot topic in climate change and ecology, and will support adapting and mitigating climate change. In this study, LPJ model modified according to features of China's natural ecosystems was employed to simulate ecosystem dynamics under A2, B2 and A1B scenarios. Vulnerability of natural ecosystem to climate change was assessed according to the vulnerability assessment model. Based on eco-geographical regions, vulnerability of natural ecosystem to climate change was analyzed. Results suggest that vulnerability for China's natural ecosystems would strengthen in the east and weaken in the west, but the pattern of ecosystem vulnerability would not be altered by climate change, which rises from southeast to northeast gradually. Increase in ecosystem vulnerable degree would mainly concentrate in temperate humid/sub-humid region and warm temperate humid/sub-humid region. Decrease in ecosystem vulnerable degree may emerge in northwestern arid region and Qinghai-Tibet Plateau region. In the near-term scale, natural ecosystem in China would be slightly affected by climate change. However, in mid-term and long-term scales, there would be severely adverse effect, particularly in the east with better water and thermal condition.