Abstract: Based on integrating the fundamental attribute and the unique property of the collaborative innovation network, this paper establishes a collaborative innovation network analogy DNA translation model through depicting external stimulus conversion progresses and behaviors of network heterogeneous agents with taking heterogeneous agents as network elements and regarding the stimulus-response mechanism as the network dynamic evolution mechanism. Using system simulation method, we analyzeget gradually into our founding about network topology structure varying rules and the interactions among structure varying rules, knowledge factors and network agents elements from multi-perspectives of the evolutionary law of the collaborative innovation network topology structure, the coupling evolution phenomenon of the knowledge and the network topology structure, distinct roles that agents play in the network and relationship between the agents’ openness and the knowledge flow efficiency. We find that: the phenomenon of small world emergences more than once through the evolution of collaborative innovation network, whose degrees and reasons are also distinctive; there exists coupling evolution between the technological knowledge and the network structure; the collaborative innovation network always be oriented towards competitive industries; the agents’ openness has an essential influence on the lifting range of the technological knowledge flow efficiency. It will propose the performance of the collaborative innovation if the subject position of industries and the agents openness degree can be strengthened during the progress of the technology creation.