Abstract: The various patterns of spatial heterogeneity in the eco-environment of the Silk Road Economic Belt of China differ greatly. In this study, a partition-integration concept was introduced to assess the ecological vulnerability of the Silk Road Economic Belt in China. To confirm the comparability of ecological vulnerability among different sub-regions, the net primary productivity (NPP) was utilized to determine the ecological vulnerability thresholds for different sub-regions. The results indicated that: (1) Fully considering the spatial-temporal patterns of the influence factors, the study region could be divided into three sub-regions: Arid Desert Ecological Region, Alpine Ecological Region and Humid and Semi-humid Ecological Regions. The new assessment method of ecological vulnerability based on the partition-integration concept was strongly operational and practical for the study region; (2) NPP with clear ecological significance was conducive to the continuous expression of ecological vulnerability, which can ensure better comparison and analysis of ecological vulnerability over the whole study region; (3) the spatial patterns of zones at different vulnerability levels differed greatly. The mild vulnerability zone was the most widely distributed, whereas the zone of slight vulnerability covered the smallest area. (4) Specific environmental protection and treatment measures should be conducted in the three sub-regions with different dominant ecological problems. The eco-environment of Arid Desert Ecological Region was mainly affected by desertification, soil salinization, wind erosion, extreme climate disasters and human activities while the Alpine Ecological Region was significantly influenced by soil salinization, freeze-thaw erosion, wind erosion and overgrazing. Meanwhile, the factors, such as water and soil loss, drought, floods, rainstorms, sandstorms and human activities played an dominate role in Humid and Semi-humid Ecological Region. These results can provide decision-making support in realizing the great strategy of the “one belt and one road” idea.