Abstract: Innovation is a new engine to promote economic development. Exploring the development of innovation is of great significance to promoting the high-quality development of the Yangtze River Economic Belt. Based on the data of 108 prefecture-level and above cities in the Yangtze River Economic Belt in 2010, 2015, and 2020, starting from the connotation of innovation and development, a comprehensive evaluation index system covering four dimensions of innovation resources, innovation investment, innovation performance, and innovation environment is constructed. Using the Topsis assessment based on the entropy weight method to measure the overall and subdimension levels of urban innovation in the Yangtze River Economic Belt. Using methods such as Dagum’s Gini coefficient decomposition to explore the spatial and temporal differences and evolution gradient characteristics of the urban agglomeration’s innovation and development level. The research shows that: (1) The innovation resources, innovation investment, and innovation performance of the Yangtze River Economic Belt are being optimized year by year, but the innovation environment shows a trend of rising first and then declining, and the high-value areas are mainly concentrated in core cities and cities with relatively developed economies. (2) The overall level of innovation continues to improve, and the spatial distribution shows a stepwise increase from the upper reaches to the middle reaches to the lower reaches. (3) The Gini coefficient of the overall innovation and development level shows a trend of rising first and then falling. The difference between urban agglomerations is the main factor that affects the imbalance of innovation development in the Yangtze River Economic Belt.