The research aims to analyze and evaluate scientific support and innovation activity in the agro-industrial complex (AIC) of Russia, identify trends and patterns of innovation processes, and design the architecture of a digital agro-ecosystem. The research presents the prerequisites for forming a digital agro-ecosystem of scientific support and commercialization of innovations, reduced to the growing need to improve the efficiency of agriculture and the quality of products. The authors developed the methodological basis for building an integrated agro-ecosystem and substantiated the synergy of interaction between the state, universities, academic institutions, and agribusiness, considering the need for innovation in the context of industries and regions. The authors constructed a model of investment contribution to the gross value added of agriculture in 2021, which shows a direct dependence and substantiates the need to improve scientific support and commercialization of innovations in the AIC. The paper identifies innovative development trends and presents methodological aspects of forming an integrated and balanced agro-ecosystem, including principles, indicators, and methods for assessing the effectiveness of functioning. The presented methodology focuses on harmonizing all institutional groups of innovative development in the region—their resources, interests, and the results of activity in temporal and spatial aspects. The practical significance of this research lies in the possibility of using a set of target metrics to assess the effectiveness of the innovation potential of the regional AIC and develop targeted mechanisms of scientific and technological development.