Innovation is the first of five development concepts, and also an important engine for the high quality development of the urban agglomeration of the middle reaches of the Yangtze River. At the same time, promoting the innovation and development of the urban agglomeration in the middle reaches of the Yangtze River plays an important role in promoting the new regional growth of the Yangtze River economic belt. It is an important and urgent task to face up to the gap of innovation and development among the cities in the middle reaches of the Yangtze River. Based on the theory of resource capability, this study constructs the evaluation index system of innovation level in the middle reaches of the Yangtze River from three aspects: the resource base of innovation, the support of innovation capability, and the output performance of innovation. The reasons for the formation of the urban agglomeration are heterogeneous, and the urbanization, GDP, the number of local colleges and universities, foreign direct investment, the number of Industrial Enterprises above the scale and so on are the factors that have a significant impact on the urban agglomeration. In order to improve the innovation level of the urban agglomeration in the middle reaches of the Yangtze River, the development of scale real economy, the development of open economy and the combination of production, teaching and research in local universities should be promoted.