The relationships among science, technology, and industry are very complicated and vary according to time. Thus, it would be almost impossible to combine the three categories in a single model. However, the linking of science, technology, and industry, which are divided according to their respective classification standards, is a starting point from which to understand how science and technology, technology and industry, and further science, technology, and industry are related to each other. This paper examines the methodology for linking science, technology, and industry, and more concretely proposes a model for analyzing science, technology, and industry in an integrated manner. This paper makes an empirical study of trend analysis of technological innovation through a linkage structure of knowledge flow between science, technology, and industry based on the classification linkage and analytic framework using scientific papers and patents. This paper uses citation analysis to analyze knowledge flow such as absorption and utilization of given knowledge, looks at the provision of knowledge to create new knowledge, and examines the use of network analysis to analyze the complicated phenomenon of knowledge flow.