The approach to the decision of a problem of management by a portfolio of innovative projects (IP) the high technology enterprise (NP) is offered. Levels of an organizational control system are considered by innovative development NP. The system of role functions of separate divisions NP on working out of innovative objects is resulted. The interrelation of the basic functions and the structure, formations defining process and management of a portfolio of IP NP, are presented in the form of IDEFO-model