Under the background of collaborative innovation, interdisciplinary research organizations due to its structural advantages should actively target frontier science and the great needs of national development, key research and strategic issues of solving the country's need, prospective issues in the frontier of science and technology and major welfare issues related to people's livelihood. And it requires reasonable localization of interdisciplinary research organizations in universities. Facing the difficulties participated in collaborative innovation, they should establish a perfect operation mechanism, play the role of collaborative innovation platform, and actively transform to collaborative innovation center scientifically and effectively.