The long-term sustainable development of rural areas determines the need to establish new development management models, based on a comprehensive analysis and assessment of development resources, taking into account the characteristics of specific territories. The aim of the study is to identify and operationalize institutional resources of the innovative development of rural areas, as well as the development of high-quality methods for monitoring and evaluation. The research methodology integrates traditional economic methods for collecting quantitative, sociological (expert) methods, as well as methods of economic statistics. The article highlights the key features of scientific discourse in the field of innovative development of rural territories, considers the main types of institutional resources, as well as existing approaches to their assessment. An analytical toolkit for monitoring and evaluating the institutional resources of the innovative development of rural territories is proposed, which allows diagnosing the range of efficiency of using the institutional resources of rural development, as well as determine the “scenario” of the institutional design of innovative development in relation to a specific rural territory. An institutional model for the innovative development of rural areas has been developed, which is a combination of five main subsystems, as well as indicators for evaluating each subsystem and the factors that influence it. It is proved that the success of achieving the goals of innovative development of rural territories is determined by the correspondence of the mechanisms of development of institutional resources and innovations (technological, organizational, marketing), as well as their focus on the long-term effects of sustainable development. Based on empirical research, the integrating role of “green” innovations as “growth points” for the sustainable development of rural territories is proved.