Conditions for applying modern approaches to the study of functioning effectiveness of corporate innovation systems are presented, the main ones of which are system, strategic and integrated approaches that will allow in practice to formulate clear guidelines for innovation development, to develop an effective algorithm of measures to achieve them and create conditions for overcome the lag in key indicators . The authors develop an organizational mechanism for implementation of strategic approach to the enterprise management system, which provides for a number of stages in the development and implementation of innovation strategy, where the corporate innovation system is the organizational basis for these processes. The monitoring of the effective functioning of this process allows to determine the internal potential of the enterprise for activating innovation activities. It is proposed to increase the level of information support for management decisions at the enterprise for innovation by introducing a methodology for analyzing the effectiveness of CIS functioning, within which stages of analysis are proposed, existing indicators are systematized, an integrated index of innovation activity is developed. Innovation activity level on the example of foreign enterprises of the automotive industry is developed that allows to present their results in a fragmented and generalized form.