The collaborative innovation of university-industry was discussed from the science of system perspective. On basis of the synergetic perspective, this paper analyzes the dynamic evolution law of innovation capability of university under the process of university-industry collaborative innovation. The research indicates that: the science of system can be used to solve the uncertainty of administrative decision. This paper established the Logistic model composed of university knowledge production capability, knowledge transmission capability, and knowledge dissemination capability on the basis of “B-Z” model. Through stability analysis and simulation, we discussed these three capabilities' evolution law and determines dominate capability elements, then the evolution law of the 3 Chinese universities in the process of University-Industry collaborative innovation will be studied by confirmatory empirical analysis. The study tried to provide policies of internal capability coordination for university-industry collaborative innovation.