In the major trend of knowledge-based economy,the innovation has become a soul of the era.The product innovation comes from technical knowledge,and the technical innovation comes from management efficiency.The major problems in the product innovative R&D management of state owned S&T enterprises were inspected and analysed,such as the imperfect project establishment,lacking of detailed working plan,R&D disconnected to engineering,unsuitable management organization structure,etc.The measure of team work contribution on information and project establishment,the construction of process evaluation system and criterion and the enhancement of stage-gate process were proposed from the view points of management system and mechanism innovation.Through innovative management to rebuild management system and incentives,all kinds of intellectual capital during project R&D management will be promoted and developed,and the enthusiasm and abilities of all kinds of talents will be stimulated to enable enterprises to retain innovative talents and increase innovation efficiency.