During the past several decades, extreme weather conditions have become frequent because of global warming. This study introduces a large-scale landscape pattern index (Shannon uniformity index and contagion index) and extreme climate index (extreme high/low temperature days and extreme precipitation days) to establish an evaluation system for the ecosystem's vulnerability, considering the unique geographical conditions (serious soil erosion and rocky desertification) in the karst mountain region of Southwest China. Next, the spatial and temporal changes in the ecosystem's vulnerability during the past 13 years were analyzed and discussed. The results indicated that the ecosystem vulnerability in the karst mountain regions belonged to the mild-moderate level, which decreased from the Sichuan-Yunnan-Guizhou zones to the marginal zones. The severe and extreme vulnerable zones were mainly distributed in the central and northern areas because of severe karst rocky desertification, low vegetation coverage, and intensive disturbance due to human activity. Conversely, the slight and mild vulnerable zones were mainly distributed in the southeastern and southwestern areas because of the high vegetation coverage, abundant precipitation, and lower disturbance due to human activity. From 2000 to 2013, the ecosystem vulnerability in the southwestern karst mountain areas increased at first and then decreased. Zones of moderate and severe increases in vulnerability were mostly concentrated in the northeastern portion of the study region, whereas zones of moderate and severe decreases were mainly distributed in the northwestern part. During the past 13 years, the temporal and spatial patterns of the ecosystem's vulnerability changes were significantly affected by human activities (different industrial GDP and population density), precipitation, topography, soil erosion, and rock desertification. This research can provide a decision-making foundation and technical support for protection of the ecosystem and restoration of the ecological environment in the karst mountain regions of Southwestern China.