Abstract: Implementing ecological restoration is an important initiative to improve the vulnerability of natural ecosystems. This study aimed to reveal the characteristics of natural ecosystem vulnerability and the sustainability of future changes in the southwest karst region of China. Based on the habitat-structure-function quantitative framework, a system of indicators reflecting the vulnerability of natural ecosystems was selected to assess the vulnerability of natural ecosystems in China's southwestern karst region from 2001 to 2022. The results showed that: (1) In general, the natural ecosystem vulnerability index (nEVI) of China's southwestern karst region was high in the central and northern parts and low in the southern and eastern parts, with a decreasing trend in the inter-annual average nEVI (R2=0.17, P<0.05); (2) In terms of different geomorphological zones, the multi-year average nEVI of karst middle and high mountainous areas was the largest (0.73) and the decreasing trend was the least significant; (3) In terms of different vegetation types, the multi-year average nEVI of alpine vegetation was the largest (0.79) and the decreasing trend was the least significant; (4) The principal component analysis indicated that the habitat indicators of NDRI and SM, the structural indicators of LAI and SHDI, and the functional indicator of GPP were the dominant factors for the vulnerability change; (5) The Hurst index and the trend analysis of Sen indicated that a total of 46.36% of the nEVI showed a weak persistent decrease. There existed a certain risk of ecological imbalance. In the future, attention should be paid to the protection of natural forests in karst middle and high mountainous areas and the sustainable management of plantation forests in other areas. The adaptive management of ecosystems should also be encouraged.