The synergy innovation of universities and enterprises in China has achieved temporary success; however， there are still some problems，such as unbalanced allocation of scientific and technological resources of universities and enterprises，single collaborative innovation mode of universities and enterprises，organizational barriers in collaborative innovation activities，low demand intensity of enterprises for collaborative innovation，etc．． In view of these deficiencies，the collaborative innovation of universities，institutions and enterprises needs to form a diversified and coexisting alliance mode，refine the contractual arrangement of deep cooperation，build a dynamic and open industrial innovation system，build an innovation carrier platform of virtual and real integration，establish and improve a regional technology transfer system，comprehensively stimulate the potential of synergy innovation from the aspects of policy supply，capital support，main part allocation，demands satisfaction，talents offering，risks control，cultural construction and so on．