Abstract Background Global warming has brought many negative impacts on terrestrial ecosystems, which makes the vulnerability of ecosystems one of the hot issues in current ecological research. Here, we proposed an assessment method based on the IPCC definition of vulnerability. The exposure to future climate was characterized using a moisture index (MI) that integrates the effects of temperature and precipitation. Vegetation stability, defined as the proportion of intact natural vegetation that remains unchanged under changing climate, was used together with vegetation productivity trend to represent the sensitivity and adaptability of ecosystems. Using this method, we evaluated the vulnerability of ecosystems in Southwestern China under two future representative concentration pathways (RCP 4.5 and RCP 8.5) with MC2 dynamic global vegetation model. Results (1) Future (2017–2100) climate change will leave 7.4% (under RCP 4.5) and 57.4% of (under RCP 8.5) of areas under high or very high vulnerable climate exposure; (2) in terms of vegetation stability, nearly 45% of the study area will show high or very high vulnerability under both RCPs. Beside the impacts of human disturbance on natural vegetation coverage (vegetation intactness), climate change will cause obvious latitudinal movements in vegetation distribution, but the direction of movements under two RCPs were opposite due to the difference in water availability; (3) vegetation productivity in most areas will generally increase and remain a low vulnerability in the future; (4) an assessment based on the above three aspects together indicated that future climate change will generally have an adverse impact on all ecosystems in Southwestern China, with non-vulnerable areas account for only about 3% of the study area under both RCPs. However, compared with RCP 4.5, the areas with mid- and high-vulnerability under RCP 8.5 scenario increased by 13% and 16%, respectively. Conclusion Analyses of future climate exposure and projected vegetation distribution indicate widespread vulnerability of ecosystems in Southwestern China, while vegetation productivity in most areas will show an increasing trend to the end of twenty-first century. Based on new climate indicators and improved vulnerability assessment rules, our method provides an extra option for a more comprehensive evaluation of ecosystem vulnerability, and should be further tested at larger spatial scales in order to provide references for regional, or even global, ecosystem conservation works.