Abstract:With the in-depth implementation of the "2011 plan", the cooperative innovation center, as an important carrier to promote knowledge innovation, technological innovation and regional innovation, plays a strong supporting role in the construction of the national innovation system. At the same time, the efficiency of Collaborative Innovation Center has been widely concerned by all sectors of society. Based on the combination model of principal component analysis and super efficiency data envelopment analysis, this paper analyses the efficiency of scientific research in the construction period of 27 industries in Jiangsu from the perspective of input resource allocation and output efficiency, and puts forward some suggestions for further promoting the development of the central high quality connotation for the competent departments, colleges and universities. With the reference of the collaborative innovation center, it provides a reference for the establishment of scientific standard of competition and exit mechanism, and makes the cooperative innovation center play an important role in the effective and rational allocation of the elements of innovation resources.