The implementation of ecological restoration programs is intensively changing the original ecological carrying capacity and the status of ecological security. To evaluate the spatiotemporal variation of ecological carrying capacity and ecological security in China’s eco-engineering areas, an indicator system of ecological carrying capacity and ecological security should be developed. This study developed an evaluation indicator system that contains 29 indicators. The indicators were generated by long-time series and multi-source data. The indicator system presents the relationship between ecological carrying capacity and ecological security and reflects the dynamic change of them in eco-engineering areas. We selected the Three-River Headwaters Region (TRHR) and implemented the Ecological Conservation and Construction Program (ECCP) as a case study. The results showed the variation of ecological carrying capacity (ECC) and ecological security (ES) in the TRHR before (2000–2004), during early term (2005–2009), and during medium term (2010–2015) implementation of ECCP, and limiting factors of ecological carrying capacity and ecological security in TRHR was analyzed. The results showed that the ECC index and the ES index were significantly increase, indicating that the ECC improved and that the ES state got better in the TRHR after implementing ECCP. The water conservation was the major factors limiting the increase of the ECC. The leading factors limiting the improvement of the ES were educational expenditure before 2010 and turned into proportion of tertiary industry and investments for ecological restoration after 2010. The implementation of the ECCP has improved the ES state but has also resulted in new problems. It provides a scientific reference for future research on the indicator system of ecological carrying capacity and ecological security in eco-engineering areas and also has vital practical significance to guide the sustainable development of ecological restoration programs.
Assessment of Ecological Carrying Capacity and Ecological Security in China’s Typical Eco-Engineering Areas