Introduction. Relevance of studying the problems of managing the innovation portfolio meso system driven by the need of forming a supportive innovation environment at the meso level. Theoretical analysis. In domestic and foreign works on the theory and methodology of project management on the management of particular importance to the innovative portfolio of projects at the meso level. State of these studies reveals new trends in the meso system. Talking about learning innovative portfolio mesoscale, the researchers noted the need to measure it in the context of territorial-cluster structure, life cycle technologies, resources, etc. Empirical analysis. The article presented and substantiated structuring innovative portfolio meso system on cluster basis of the example of the Saratov region, which required a quantitative analysis of regional clusters of innovative projects in stages of development in the Saratov region in 2011–2013. and analysis of the number of organizations involved in the development of innovative projects Saratov region for 2011–2013. Results. Due to the analytical, identified problems in an innovative portfolio of Saratov region, and propose a scheme of management of innovation portfolio at the meso level according to the steps of the process of «leveling» (portfolio formation) and «monitoring and control».