The study area of this paper is the Qinghai alpine agricultural mountain area. An ecological security early-warning model is used to identify the early warning signs of ecosystem destruction, environmental pollution and resource depletion in districts and counties from 2011 to 2018. A combination of qualitative and quantitative early-warning models is used to predict the existence of hidden or sudden advance warnings. The grey (1, 1) model (GM) is used to predict the evolution trend of ecological security warning situations from 2019 to 2021. On this basis, GIS technology is used to analyze the spatial pattern changes in three periods. The results show that from 2011 to 2018, the ecological environment in Qinghai’s alpine agricultural mountainous area gradually improved. In 2018, the ecological security early-warning values of all districts and counties were greater than the 2011 values. However, in 2018, the ecological security early-warning levels of PA, LD and HZh (PA, LD and HZh refer to Ledu District, Ping’an District and Huzhu Tu Autonomous County respectively.) were in the “good” ecological early-warning state, while the ecological security levels of other cities were still in the “moderate” or “mild” ecological warning state. According to the prediction results, the early-warning level of ecological security in Qinghai’s alpine agricultural mountainous areas will improve further in 2021, with the “good” states dominating. From a spatial perspective, the ecological environment in the northeast region is better than that in the southern region, and the internal differences in the ecological security early-warning levels tend to narrow. Thus, we propose that areas with different ecological security levels should focus on the management and protection of the ecological environment or carry out ecological restoration or reconstruction. The aim of this paper is to provide a reference for the improvement of the ecological environment in general and the sustainable development of the economy and society as well as the ecological environment of alpine agricultural mountainous areas in particular.