According to the comparative analysis of regional innovative competence among six provincial capital cities in central China, it fits the “Rise of central China” national strategy, and also in response to development policy of national innovative cities construction. Based on knowledge flow related assessment system of regional innovative competence, this research evaluated six provincial capitals, Zhengzhou, Hefei, Changsha, Wuhan, Nanchang and Taiyuan by processing data from 2007 to 2012. The result was combined with the six cities innovative policy in recent years, by comparing and analyzing all aspects of knowledge flow procedures, to finally sort out effective policies and measures to the construction of regional innovation. This research shows the differences of RIS among the six cities and tends to explain why through policies. It provides more experience for others to understand about regional innovating competence and the development trend.