The national key ecological function areas in the western region are not only fragile in ecological environment, but also lagging in economic development and social public services. In the past several decades, the contradiction between ecology, economy, and society caused by human behavior has aroused widespread concern. Therefore, exploring the evolution characteristics of ecological-economic-social (EES) system coupling and coordination degree in the national key ecological function areas is of great significance for achieving sustainable development goals and building a beautiful China. In this paper, we use the coupling coordination model, scissors difference model, coupling degree model, and vector autoregressive model (VAR model) to explore and analyze the dynamic evolution of the coupling coordination degree of the EES system in the Altay region from 2007 to 2019. The results show that:(1) from 2007 to 2019, the overall coupling coordination degree of the Altay region in Xinjiang showed a rising trend, which was evolving from a moderate imbalance (0.271) in 2007 to a mild imbalance (0.371) in 2019. The development level of the ecological system and the development level of the economic system and the social system presented a trend of "X". Specifically, the development level of the economic system and the social system continued to rise, while the ecological system decreased slightly. (2) The scissors difference in the evolution rate of "the economic system and the social system" as well as "the ecological system and the social system" fluctuated significantly after 2014, while the scissors difference in the evolution rate of "the ecological system and the economic system" tended to be stable. The coupling degree of "the ecological system and the economic system" and "the economic system and the social system" showed an initial transition from disorder to order. (3) According to the analysis results of impulse response function and variance decomposition, the improvement of the coupling coordination degree of the EES system in the Altay region was the result of the interaction of the three systems. To be specific, in the early stage, it was mainly driven by the social system and the economic system, while in the late stage, it mainly depended on the improvement of the ecological system to promote the coupling coordination degree of the EES system. The research showed that the national key ecological function areas should focus on reducing the stress intensity of the economic system on the social system and the ecological system in the future, so as to achieve the coordinated development of the three systems.