In the economy of the Russian regions, the situation has developed in such a way that their development requires new approaches and technologies for managing processes based on knowledge, the latest achievements and world experience. The indicated trend implies the need to develop and justify competitive development strategies based on the competitive advantages available in each region, reflecting the specifics of their potential. Innovation clusters play a special role in this case, influencing regional growth due to their flexibility and adaptability to the needs of territories. The development of these clusters provides access to knowledge, increases interest in the introduction of innovations and technologies, and also leads to cost reduction and the implementation of special smart specialization strategies. Over the past fifteen years, clusters have been considered one of the most advanced forms of organizing efficient production, combining science, research and development, innovation, environmental solutions and technologies. Therefore, for the domestic economy and its individual sectors of strategic importance, in particular the agricultural sector, it is necessary to substantiate the scientific foundations of the transition to a cluster model of development and its implementation at the regional level. This article examines the theoretical issues of substantiating the need for the formation of sustainable agricultural production on the basis of innovative development, clustering and cooperation, examines the feasibility of functioning of cluster structures as a special innovative form of cooperation and integration in the agricultural sector.