Under the background of the continuous progress of China’s agricultural reform, the development of characteristic agriculture is an important field of agricultural development in the country and even the world. Yunnan has unique advantages in geography, location, climate, and human resources, and has unique conditions for the development of agriculture with plateau characteristic. However, the sustainable development of agriculture with plateau characteristic is affected and restricted by many factors. How to promote the sustainable development of agriculture with plateau characteristic is an important research topic, and it is also the main purpose of this study. Therefore, through literature analysis and investigation, this study studies the advantages and disadvantages, development status, main problems, countermeasures and suggestions, macro development direction, and theoretical research methods of characteristic agriculture in the Yunnan plateau. This paper analyzes the advantages and disadvantages of the Decision-making Trial and Evaluation Laboratory (DEMATEL) and the Adversarial Interpretation Structure Modeling Method (AISM) and proposes to combine the two models to make up for each other and improve the accuracy of model analysis. On this basis, a set of identification and evaluation systems of factors affecting the sustainable development of agriculture with plateau characteristic is established, which can comprehensively and accurately identify and evaluate various influencing factors, and provide a scientific basis for the sustainable development of agriculture with plateau characteristic. Finally, combined with the relevant statistical data of Yunnan Province from 2009 to 2020 and many results calculated by the model, the factors affecting the sustainable development of agriculture with plateau characteristic were comprehensively analyzed. The results show that transportation, environment, and insurance support factors are the root factors that affect the sustainable development of agriculture with plateau characteristic, while the regional economy, scientific and technological support, and the development of agricultural enterprises are of high importance. Financial support, the level of agricultural mechanization, the quality of labor, and other factors can not be ignored. Finally, according to the results of the analysis, the corresponding policy recommendations are put forward to provide a reference for the sustainable development of plateau characteristic agriculture in Yunnan Province.