Abstract:This paper uses complex network theory and social network analysis to study the scientific research innovation and cooperation between universities in China, mainly based on papers published by 2138 high colleges in 2014 years. The research indicated that the scientific research innovation and cooperation network is scale-free network with robustness and fragility, and the network isn’t centralized, small group phenomenon is not obvious; the core of the network is dispersed. The core region of the network includes 78 colleges, such as Peking University, Renmin University of China and Tsinghua University. there are 16 subgroups in the network that communicate closely, these groups could be divided by province in China, For example, some subgroups are in Guangdong province, some are in Beijing, and others may be in Jiangsu province. There is one or two comprehensive universities in the core region. This paper also found that cooperative groups showed significant academic characteristics. Comprehensive universities, medical universities and universities of science and engineering are more tend to cooperate than others.