This paper demonstrates the application of cognitive modeling methods to study problems relating to the functioning and advancement of a strategy for the development of rural areas. Rural areas play a vital role in human life; they have enormous economic, natural, demographic, historical, and cultural potential, and their revival ensures the achievement of the United Nations Sustainable Development Goals in the field of SDG 2: “End hunger, achieve food security and improve nutrition and promote sustainable agriculture”. The relevance of the study lies in the need to develop approaches in order to improve the efficiency of agriculture and to ensure the sustainable development of rural areas. The goal was to use cognitive modeling tools to understand the cause-and-effect mechanism of ensuring sustainable development of rural areas and analyze their possible development under the influence of internal and external factors to select the best strategy for sustainable development. Based on 24 selected quantitative and qualitative indicators, a cognitive map “Sustainable Development of Rural Areas” was constructed, and an analysis of 351 cycles of the cognitive model was carried out, among which 286 positive and 65 negative cycles were observed, indicating the structural stability of the model. Computational experiments were carried out using pulse and scenario modeling; the results are presented and visualized in the form of five scenarios for complex systems development. The results of this study can be used as decision support tools for substantiating strategies and developing policies for the balanced development of rural areas.