Using the regional innovation system as the analytical framework, this thesis studied the dynamic efficiency that leads to the innovation ability difference between provinces empirically, and explained the reasons of system that result in the regional difference and affect the innovation elements’ agglomeration according to the innovation data relates to provinces. By using the number of authorizations of applications as the index to measure the innovation output, this study found out that there is a big difference between the eastern, central and western parts of China, though the difference between the central and western parts is not that obvious, the eastern part’s innovation output is far more than the rest areas. See from the various areas, the areas located in coastal developed cities or populated with universities and research institutions are usually equipped with higher R&D investment and more competitive innovation ability.