<p>This article presents the results of research on complex natural-social-economic objects—agrarian-territorial systems (ATS) of Russian regions—through the lens of the knowledge economy. The practical implementation of a systems approach is focused on solving problems of agricultural development by integrating knowledge creation, diffusion, and application. We identify four key ATS subsystems—agricultural natural, agricultural production, agricultural economic, and social—and posit that their evolution is increasingly driven by innovation and intellectual capital. The research hypothesis was not only about the possibility of identifying general knowledge-based development patterns for diverse ATS but also about the feasibility of constructing a novel toolkit for their formation. The methodology combines systems theory with multivariate statistics to analyze both stationary and dynamic aspects, enabling the identification of characteristic features for constructing development patterns. The main result is the development and testing of a knowledge-centric pattern-constructor for ATS development trajectories. Its construction is based on a retrospective analysis of multivariate trajectories and the formation of differentiated target benchmarks for its key subsystems, informed by their knowledge and innovation capacity. The proposed approach and toolkit can be used to govern knowledge flows and build intellectual capital within ATS, thereby infusing knowledge economy principles into the development and updating of agricultural policy and its practical implementation.</p>