The multi-scale comprehensive analysis of ecological risk assessment is of great significance to environmental management and risk-based decision making. This study takes key monitoring counties with frequent landslides in the Three Gorges Reservoir area as examples. Based on the three-dimensional model of "Hazard-Vulnerability-Damage", the random forest model was applied to evaluate the landslide hazard, the landscape pattern index was selected to characterize the ecological vulnerability, and the habitat quality was used to calculate the potential ecological damage. We carried out the ecological risk assessment of landslide disasters under the grid, administrative, and sub-watershed scales, and proposed risk management measures suitable for each scale. The results indicate that areas with higher ecological risk levels were concentrated along the banks of the Yangtze River at any scale, since the construction of the Three Gorges Reservoir area had a greater impact on the ecological risk of landslides in the study area. The risk distribution results of each two scales were comparable to a certain extent, while certain differences existed in the results of the overlay of three scales. The evaluation result of the sub-watershed scale was preferable than the other two scales under the premise of ensuring the integrity of the ecological structure, and was more suitable for the Three Gorges Reservoir area. The eastern part of the study area had a relatively homogeneous type of risk prevention, while the western part had a variety of types of risk prevention, which required refined management. This study adds a multi-scale comprehensive assessment example, and lays a theoretical and practical basis for future research on ecological risk assessment of landslides in the entire Three Gorges Reservoir area.