Biological invasion poses a major threat to biodiversity and conservation efforts in protected areas. The Greater Shennongjia Area (GSA) is one of China's 16 key areas for biodiversity, as stated in the China National Biodiversity Conservation Strategy and Action Plan. However, the local authorities lack appropriate data on the extent and impact of exotic species in protected areas, as well as lack the capacity and motivation to properly plan for exotic species strategy and action plan to support both prevention, control as well as management of exotic plants in their jurisdiction. In addition, while most previous studies have focused on exotic species in protected areas, little effort has been devoted to specifying which environmental factors contribute to the difference between protected and non-protected areas. Here, we explored the current distribution pattern of the richness and abundance of exotic species in relation to environmental variables within the GSA. In total, we found 84 exotic plant species, of which 41 exotic species within the protected areas, in 64 genera and 27 families, predominately from Asteraceae, Fabaceae, and Poaceae. The generalized linear mixed models (GLMMs) revealed that the protection status and the distance to human settlements were the most important predictors of exotic plant richness and abundance in the GSA. Our results showed that the average exotic plant richness and coverage in the protected areas were 22% and 31% lower than outside the protected areas, respectively. Such differences were probably the result of anthropogenic activities (e.g., proximity to human settlements and the proportion of cropland). Although protected areas provide an important barrier against plant invasions, invasion may be a tricky issue for protected area management in the future. The Alliance of Protected areas in Western Hubei and Eastern Chongqing will need to further consider stringent control and management strategies for the entry of exotic species into protected areas to effectively maintain the continuity and integrity of the GSA's biodiversity and ecosystems. Our results provided guidance and support to enhance the capacity of scientific and effective management and sustainable development of the Shennongjia World Natural Heritage Site and other protected areas.