Understanding the evolutionary characteristics of innovation network structure can improve urban innovation and regional construction. Urban innovative development is affected by various factors, which can be analyzed via models of innovation networks. We establish a multi-criteria evaluation system of innovation capability and use an improved gravity model to construct an innovation network for 2015–2018, employing social network methods to analyze structural characteristics and spatial patterns. Results show that: (1) The innovation of cities in the urban agglomeration in the middle reaches of the Yangtze River has gradually increased, with an accompanying increase in the complexity of innovation networks. The cities of Wuhan, Changsha, and Nanchang are located at the absolute core of this network, which exhibits a Matthew effect, and has a triangle integration mode of growth. (2) The attraction of innovative resources and the promotion of individual innovation are increasing every year within the cities. The aggregation pattern of innovation shows a multi-core state in the urban agglomeration in the middle reaches of the Yangtze River, but the innovation radiation pattern has changed from a single center to a double center. (3) Multiple spatial innovation axes are seen in the network, with a location and direction consistent with the urban agglomeration’s development axis in the Yangtze River’s middle reaches and a triangle integration growth mode. Policy implications are proposed for regional innovation and development, and our results can provide future policy guidance and direction for governmental entities and other stakeholders.