It is only possible to manage innovation effectively when this activity is viewed as an integral system that pulls together all processes of developing, creating and operating innovative facilities into a single innovation project. In order to manage such projects effectively, appropriate methods, procedures and indicators of management analysis need to be developed and applied. This type of management analysis is of comprehensive nature and includes the analysis of innovation performance, investment analysis, competitor analysis and marketing analysis. The main purpose of such analysis is to provide the managers and owners of the company with full, reliable and quality information about its innovation performance, untapped reserves and opportunities for their mobilization. When designing a system of indicators for integrated management analysis of innovation performance, priority is given to science and technology indicators and those of competitiveness, quality, heuristic and commercial potential of innovations. The results of such analysis could be used for substantiating the choice of alternative innovation projects that meet the criteria of this or that area of analysis; identifying the possibility of applying non-standardized analysis methods when conducting integration procedures and selecting the most successful innovation project; obtaining an overall assessment of innovation performance, trends and development factors.