Knowledge exchange and transfer are very important in a R&D environment driven by knowledge and technology. This paper aims to study the structural evolution features of the Collaborative Innovation Network (CIN) of college students from the perspective of knowledge flow. The knowledge flow among the collaborative innovation relationships of college students has not only produced many innovation achievements and high innovation conversion values, but also promoted knowledge sharing and increased regional economic benefit. To figure out the structural evolution features of CIN from the perspective of knowledge flow, at first, this paper explores the network-shaped knowledge flow pattern, constructs a model that can reflect the innovators’ citation of innovation knowledge and the interaction between related factors and their interaction space, and analyzes the distance attenuation of knowledge flow of CIN and its evolution trend. Then, this paper combines the structure of CIN with the evolutionary game, builds an Evolutionary Game (EG) model of CIN, and analyzes the evolution law of college students’ collaborative innovation behavior in CIN. At last, this paper gives experimental results and verifies the validity of the proposed model.