The econometric relationship of R&D expenditure and patent output in both enterprises and public R&D institutions is analyzed by co-integration and Granger causal analysis of econometrics. The results indicate that the relationship between R&D expenditure and patent output in both enterprises and public R&D institutions has a stationary long-run equilibrium tendency. Furthermore，the output efficiency for different patents presented different by the two main innovation bodies. Public R&D institutions have an advantage on the invention patent output， while enterprises have an advantage on practical patent output.