The interaction path maps between R&D institutions of transnational corporations and Regional Innovation System (RIS) of China are established, and the relevant hypotheses from the perspectives of knowledge flow are put forward. On the basis of it, the enter methods are adopted to carry out empirical analysis on interaction path between R&D institutions of transnational corporations and RIS of China and interaction coefficients are drawn out. The research indicates that (1)technological innovation resources investment capacity and roles of enterprises have the indirect influences on bilateral interactions; (2) regional innovation environment, technological innovation output capacity of enterprises, and learning capacity of regional enterprises are positive related to bilateral interactions, however, regional diffusion capacity and regional technological innovation support capacity have the negative influences on bilateral interactions;(3) the integration degrees between R&D institutions of transnational corporations, regional cultures, law, and regulations have the significant influences on bilateral interactions. The conclusions possess the guiding significance for making the full use of transnational corporations' R&D investment and constructing RIS of China.