Large-scale water conservancy projects benefit human life but have modified the landscape and provided opportunities for alien plant invasions. Understanding the environmental (e.g., climate), human-related (e.g., population density, proximity to human activities), and biotic (e.g., native plant, community structure) factors driving invasions is essential in the management of alien plants and biodiversity conservation in areas with intense human pressure. To this end, we investigated the spatial patterns of alien plant species distribution in the Three Gorges Reservoir Area (TGRA) of China and distinguished the role of the external environment and community characteristics in determining the occurrence of alien plants with differing levels of known invasion impacts in China using random forest analyses and structural equation models. A total of 102 alien plant species belonging to 30 families and 67 genera were recorded, the majority being annual and biennial herbs (65.7%). The results showed a negative diversity-invasibility relationship and supported the biotic resistance hypothesis. Moreover, percentage coverage of native plants was found to interact with native species richness and had a predominant role in resisting alien plant species. We found alien dominance was mainly the result of disturbance (e.g., changes in hydrological regime), which drove native plant loss. Our results also demonstrated that disturbance and temperature were more important for the occurrence of malignant invaders than all alien plants. Overall, our study highlights the importance of restoring diverse and productive native communities in resistance to invasion.