This paper regards patent applications data from 2000 to 2012 on Wanjiang City belt as the representation of the regional innovation output. Theil index is used to detect each city's innovation ability and analyze the difference of them. What the research shows is that the innovation ability of southern area with Wu Hu as the core is weaker than the north area with Hefei as the core. This can be known from the minus Theil index during 2000 to 2012 of patent applications in the southern area, whereas the plus index in the northern area. However, the Theil index of two areas is approaching to zero, and the Theil index of the southern area is from the negative into the zero, which indicates that the innovation ability in the southern area is developing faster. Overall, the unbalanced situation of Wanjiang City belt’s innovation ability will continue.