This paper establishes evaluation indexes system which contain 6 dimensions and 49 indicators on governance of regional innovation system based on its connotation, public governance theories and research in more than 100 references, and then measures and analyzes the regional innovation governance index in the year 2014 by VIKOR method. Meanwhile, the paper studies the relationship between governance of innovation system and economic development, and also its governance dimensions and industrial structure development through the regression model in years 2011-2014. The results show that the governance development of regional innovation system are not balanced, where existed two more obvious differentiation. Secondly its dimensions development are not balanced and shows a non-synchronous character accompanied the governance index of innovation system. Again, the governance of regional innovation system has significant positive driving effect on economic development after eliminating the "three carriages" effect and the most significant effect in the 2 year lagging. Moreover, multiple governance dimensions of regional innovation system have significant positive effect on the development of industrial structure, however, one governance dimension does not have a direct positive effect. Lastly, the paper puts forward policy suggestions.