This paper uses the entropy method，the global natural breakpoint method，and the analysis of hot and cold spots to study the evolution of the spatiotemporal pattern of urban innovation capacity in the Yangtze River Delta and its phase characteristics. The research finds that the overall performance of innovation ability is a growth trend，and the influence degree of basic dimensions on innovation ability is innovation basic environment＞technological innovation＞innovative talents＞industrial cluster＞market openness. Changes in the ranking of cities in the Yangtze River Delta in terms of innovation capability can be divided into three types，namely，6 cities in the top ranking such as Shanghai，12 cities in the middle ranking such as Hefei，and 9 cities in the lower ranking such as Yancheng. The overall innovation capability is divided into four levels，namely high-level cities，high-level cities，low-level cities and low-level cities. The innovation capacity of cities in the Yangtze River Delta from 2000 to 2019 can be divided into a rapid growth stage from 2000 to 2006，a steady growth stage from 2007 to 2010，and a slow growth stage from 2011 to 2019.