Stability is an important characteristic of the ecosystem that determines the rise and fall of ecosystems. Ningxia Zhongwei Shapotou National Nature Reserve is a nature reserve in an arid desert area, with the desert as the background. This protected area has the characteristics of vulnerability (ecology and environment), transition (grassland to desert and desert to city), and complexity (coexistence of natural and artificial ecosystems). Evaluation of ecosystem stability in Shapotou Reserve is of great significance for maintaining the ecological security of the southwestern margin of Tengger Desert and sustainable and healthy development (social and economic) of Zhongwei City. On the basis of summarizing the research on the stability evaluation of ecosystems at home and abroad, in this paper, we have defined the three-dimensional connotation of stability (resilience, resistance, and succession stability). We also performed a demonstrative assessment of the ecological stability of Shapotou National Nature Reserve from three aspects:defined three-dimensional stability (resilience, resistance, and succession stability), constructed evaluation indicators (principle and logical framework), and established assessment methods (traffic light comprehensive assessment method). The results were as follows:(1) In the past 20 years, of 19 individual indicators, most of the indicators tended to improve, a few deteriorated further, and two remained basically stable. (2) Factors that affect the stability of the ecosystem were changed from community composition to habitat conditions. In the six key years of 2001, 2005, 2007, 2010, 2012, and 2014, resistance or resilience contributed the most to ecosystem stability. (3) The overall ecological stability index of protected areas increased from 0.41 to 0.661, and the trend was from critical point to stable point. Overall, the stability of regional ecosystems has increased. This was mainly due to the implementation of long-term sand control and ecological restoration projects, large-scale reforestation projects, ecological monitoring and maintenance, and large-scale irrigation of the Yellow River water.