Regional innovation system is not just an input-output system as the traditional economics regards.In fact,the efficiency of regional innovation not only includes the efficiency of resources allocation with static equilibrium by market mechanism, but also has the network and overflow effect characteristics. At the same time, the efficiency possesses the institutional form feature under the regional institution mechanism.Furthermore, based on the possible boundary of regional innovation efficiency, two patterns of efficiency enhancement including the original efficiency and later-coming one are explored.