Based on dynamic monitoring data on China’s population, by using complex networks, spatial analysis and mathematical measurement, this study reveals the spatial characteristics and influencing factors of the network of flows of highly educated talents in the Yangtze River Delta region from the national and local perspectives. In the two perspectives, the network has strong isomorphism and certain differences. The in-flow of highly educated talents from cities with high administrative levels and more developed economies to Shanghai constitutes the core of the entire network. From a national perspective, highly educated talents tend to converge to the Yangtze River Delta region. From a local perspective, it was found that these talents cluster towards a limited number of cities in the region. From both perspectives, the flow network has developed into a “core-periphery” progressive hierarchical structure, with Shanghai becoming the sole core city. There is little difference in the influencing factors of talent mobility from both macro and meso perspectives. Highly educated talents would frequently flow between cities with strong economic development levels, and cities with high education level, scientific and technological level, complete infrastructure, and good aesthetics. However, geographical distance still plays a hindering role in the flow of highly educated talents, and factors such as cultural identity, institutional, and social modality differences among regions also have a certain effect on the flow of these talents.