With the development of economic globalization, urban agglomerations have become growth poles and core areas of economic development. By building knowledge innovation networks in urban agglomerations, we can effectively improve the strength of inter-city knowledge innovation links and better realize the integrated and synergistic development of the region. This study selected core cities in the Yangtze River Delta urban agglomeration as the study area, constructed the knowledge innovation network based on inter-city dissertation cooperation data from 2010 to 2020, and analyzed the characteristics and evolution of its knowledge network by combining social network analysis and geospatial analysis. The research results show that: (1) with changes in policies and investment in scientific research and innovation, intra-regional thesis cooperation in the Yangtze River Delta urban agglomeration has been increasing and the scale of the knowledge innovation cooperation network is growing; (2) in addition to the core cities radiating innovation resources outward to drive the development of other node cities, other cities are continuously improving their own innovation capabilities, taking the initiative to strengthen knowledge innovation cooperation with core cities and enhancing their own position in the network; (3) there are no longer isolated cities within the Yangtze River Delta urban agglomeration, and a multi-core knowledge network structure centered on Shanghai, Nanjing, Hangzhou, and Suzhou has initially formed, but the network is still spatially heterogeneous; (4) there are still problems within the Yangtze River Delta urban agglomeration such as uneven development of knowledge innovation and low participation of peripheral cities, which need to be addressed jointly by all regions. The article concludes with some suggestions for countermeasures to provide a reference for the Yangtze River Delta urban agglomeration to continuously strengthen intra-regional knowledge cooperation in the future, enhance regional competitiveness, and ultimately achieve synergistic development among cities.