The relevance of the study is conditioned by the need to apply a systematic approach to the investigation of agricultural production features as a complex dynamic structure that functions in an unstable market environment and depends on the influence of natural changes. In this regard, this study aims to identify socio-economic, natural, and environmental factors that affect the sustainable development of agricultural sectors, as well as predict the impact of material, technological, and climatic factors on the health and stability of the entire system. The leading method for studying this problem is the method of a systematic approach, which allows investigating agricultural production as a complex dynamic structure that functions in an unstable market environment and depends on the influence of natural factors. In addition, this study involved the following research methods: the method of structural analysis, comparative, statistical, and deduction methods, classification method. The study presents the factors directly or indirectly influencing the development of northern agriculture, predicts the impact of these factors on the stability of the system, and shows possible ways to overcome the negative impact. The regional management system directly affected the level of food self-sufficiency of the Sakha Republic. To improve the current situation, it is necessary to review the mechanisms of interaction between state institutions and agricultural producers. Furthermore, there is an entire list of factors that negatively affect the functioning of the agricultural sector of Yakutia. The situation requires an immediate design of a policy for the development of rural areas through the socio-economic development of villages in the region. The research materials are of practical value for the governing bodies of the agro-industrial complex of the Republic of Sakha (Yakutia), as well as teachers and students studying the issues of sustainable development of agriculture.