Organizational and economic mechanism of investing in the production is updated with a new element — controlling. Controlling is aimed at efficient development of the system providing the control system with organizational, economic and managerial methods and productive investment and management instruments in general through registering resources and results of the region organization activity. The authors suggest the model of controlling operations of investment and innovative activity in the region. They propose the approaches to designing the strategy map of organizations engaged in investment and innovative activity on the basis of the balanced scorecard, which shows promising areas of investment and innovation process of the object. The specific feature of this model is the use of the innovations that characterize the management of investment and innovation activity from the point of view of development process resourcing and the prospects for marketing strategies application. The role of the innovation component is to increase the efficiency of resource use while developing and introducing innovations in investment and innovation activity of the regional organizations.