Science and technology enterprises have become an important power to promote the regional science and technology innovation in Xinjiang, due to its own conditions, the cooperative innovation has become an effective way to enhance the innovation capability of Xinjiang science and technology enterprises.The typical enterprise interviews, selected 10 companies on the issues involved in the interview conducted a survey and found that, at present there are still many problems of collaborative innovation activities: from research in perspective, barriers to collaborative innovation problems mainly include: the study of the existing management system has restricted the actual party technical requirements of R & D results and the enthusiasm of enterprises, participate in collaborative innovation research institutes, enterprises out of profit and risk control lead to a single, R & D capability and knowledge transfer can lead to low synergy efficiency is low; from the perspective of the external environment, but also the lack of promoting enterprises to become the main collaborative innovation the government policy and clearly support the collaborative innovation of science and technology policy and economic measures, and the financial intermediary and the intermediary service of science and Technology Branch Holding the strength is insufficient, etc..To this end, this paper puts forward the corresponding countermeasures and suggestions from the perspective of the three party participation in the main body and the external environment.