From the empirical analysis of interprovincial panel data, some discovery that the division and cooperation of R&D Institutes have different impacts on new products output and invent patents output are put forward. We argue that he basic research of universalities and independent research institutions has no direct positive effects on new products output; however, it upgrades the marginal contribution of R&D expenditure as a moderator and exhibits positive effect on patents output. The cooperation of universities industries has no effects on patents output, however, it has positive effects on new products output. Furthermore, the paper argues that R&D activity of firms has been linked with more interdisciplinary, diverse and innovative network system in open innovation environments and the dynamic balance of division and cooperation mechanisms of R&D Institutes in innovation system should be paid more attention.