Under the dual background of the acceleration of urbanization and the requirement of sustainable development, people are paying more and more attention to regionally ecological security. In this context, landscape ecological risk assessment could evaluate the regionally ecological environment from the perspective of landscape pattern and ecology, and it is a crucial way to construct regionally ecological security pattern. Previous attempts to evaluate landscape ecological risk mainly focused on land use and the calculation of landscape index, overlooking the impact of topography. The Karst Fault Basin is located in the middle and upper reaches of the Pearl River and the Yangtze River, with complex topography and fragile ecological environment. Here, taking the Karst Faulted Basin as the research object, we selected 11 evaluation factors from three dimensions of nature, society and landscape pattern to construct an evaluation index system of landscape ecological risk. The factors' weights were determined by spatially principal component analysis (SPCA) and mathematical statistics, and the spatio-temporal evolution pattern of landscape ecological risk in the study area from 2000 to 2020 was evaluated. Furthermore, based on terrain niche index derived from Digital Elevation Model (DEM), the topographic distribution indices of each ecological risk grade in the study area from 2000 to 2020 were calculated, and the relationship between landscape ecological risk and topography in the Karst Faulted Basin was systematically revealed. The results showed that:(1) from 2000 to 2020, the landscape ecological risk level of the Karst Faulted Basin presented a downward trend, and the overall level of ecological environment improved. The change of landscape ecological risk demonstrated strongly spatial and temporal heterogeneity. In 2000 and 2005, the landscape ecological risks in the study area were mainly medium, relatively high and high, and concentrated in the north and some parts of southern study area. After 2010, the area of high risk region decreased significantly, while the area of low risk region increased significantly. However, the landscape ecological risk level of some southern districts and counties showed a trend of rising instead of decreasing. (2) The landscape ecological risk levels of different land use types decreased significantly except for construction land in past 20 years. In 2020, the cultivated land, forest land and grassland were mainly distributed in areas of low and relatively low risk level, while the area of construction land in high risk regions was still as high as 43.43%. (3) The changes of landscape ecological risk in different topographic gradients presented significant differences over time. At the early stage of the study period, all risk areas had strong terrain selectivity. Low and relatively low risk regions were mainly distributed in the middle and low terrain intervals, and high risk areas tended to be distributed in the high terrain intervals. As time went by, the topographic selectivity of different risk regions declined, indicating that the impact of terrain on landscape ecological risk gradually decreased, and the influences of human activities on landscape ecological risk became increasingly obvious. Our analysis can provide a reliable scientific basis for optimization of landscape pattern, ecological protection decision and further development and construction of the Karst Fault Basin.