Abstract:The paper constructs the evaluation index system of comprehensively innovative capacity in the Industrial transfer demonstration area of the cities along the Yangtze River in Anhui Province, using the Series Catastrophe Theory, evaluating the comprehensive innovation ability of regional city quantitatively. The research indicates the comprehensively innovative capacity of Hefei and Wuhu at a high level, other city’s innovative capacity exist difference, some at a medium level. The paper puts forward some countermeasures to improve the innovative capacity of the cities, basing on the establishment of innovation system, cultivating many more innovative plots, forming the core city radiation and regional city linkage development mechanism, seeking the upgrading of the industrial transformation and scientific effect on the innovation input and output, provides a new perspective study and reference on the same research.