Along with the continued growth, the production environment of enterprises have also been changed. While the industrial competition has been continuously increased, R&D and Innovation become necessary for an enterprise to survive. In the past, due to the lack of the capitalization and R&D investments of the domestic industries. Universities and the like R&D institutes thus played an important role in technology transfers. The purpose of this investigation is to study the various firms in the industrial zones of Taiwan, how is the technology transfers and innovation sources diffused among the firms and those Universities as well as other R&D organizations of Taiwan. This study also intends to investigate the possible connection between the innovation source of firms and their location. Our investigation discovered that the firms in the technology science park are more innovative aspiration and move willing to adopt innovations. Through universities and R&D institutes as innovation sources, it diffused among firms and all kinds of R&D institutes by the appearance of industry-university agglomeration. Although the firms in the export processing zones and other non-technology science parks have connection with universities and R&D institutes mostly through informal linkage relationship. Their appearances and desires of innovation diffusion were less than those firms in the technology science park. This study also discovered a strong connection between the firm's innovation behavior and the universities and R&D institutes by use the statistical test. Evidence also show that there is connection between the firm's innovation behavior and the firm's agglomeration.