Abstract: Healthy development and evolution of scientific knowledge network is important to cities’ innovation. This paper use the data of the paper cooperation between 25 cities in the YangTze River Delta from 2000 to 2015, analysis the dynamic evolution of whole network and ego network combining the indicators of structure、spatial characteristics and complexity. Major findings include: (1)Function in the topological indicators of the whole network are power-low functions. The network is expanding, weights、density and cluster coefficient are increasing every year. (2)The trend of integrated network is evolving to “small-world”, which is more obvious after 2008 and has scale-free characteristic. (3)Nodes Degree distribution of city ego network obey the bell curve which means the fairness of cooperated chances. The nodes and edges distribution of weight are consistent with the Pareto distribution, which means the agglomeration of the cooperated resource. Spatial mode of network are hierarchical diffusion and multiple centrality structure. (4) City ego network evolve from cooperation to research. The speed of evolve will be more far. Research cities are the major power of the network development and evolution lately.