Innovation is the driving force of economic and industrial development, and the evaluation and research of regional innovation capability is an important way and method to identify regional innovation ability. Through the establishment of a regional innovation capability evaluation index system, the global entropy method is adopted to dynamically evaluate the innovation capacity of the Yangtze River Delta region from 2016 to 2020 by using the overall thinking. It is found that the innovation capacity gap in the Yangtze River Delta Region is large, and there is an imbalance in regional innovation and development. The analysis of the changes in the structure of innovation capacity in each region is conducted, and it is found that the innovation output and innovation results are the shortcomings of the innovation capacity in the Yangtze River Delta Region.