Statistical data from 13 branches of Chinese academy of sciences was analyzed to study the collaborative innovation activity in research institutes based on the classical "B-Z" reaction model in the complex system theory, from the three-dimensional perspective of evaluation scale (knowledge production, knowledge dissemination and knowledge transfer).It is indicated the apparent disparity among activities of scientific research institutes; however, the activity maintains consistent with the external input. Meanwhile the collaborative innovation active of eastern region are significantly higher than the central and western regions. There are differences in knowledge production, knowledge transfer and knowledge dissemination within each branch of the research institutes; And the west shows the weakest activity. According to the 13 branches of Chinese academy of sciences’ running system in the overall performance of collaborative innovation study, those institutes, in this paper, are divided into 3 types by the differentiation trends, namely, activity type, smooth type and the general type.