Abstract:This paper combines the innovation chains and innovation networks, and explores the complexity characteristics of urban networks in the Guangdong-Hong Kong-Macao Greater Bay Area from two dimensions of vertical process linkages and horizontal regional networks of innovation chains. Based on the patent transfer data of "9+2" and 30 external provinces in the Guangdong-Hong Kong-Macao Bay Area from 2005 to 2019, social network analysis with negative binomial regression and gravity model were used to empirically prove the influencing factors of urban innovation networks and its innovation chain synergy capacity. The results shows that:1) Cities of The Guangdong-Hong Kong-Macao Greater Bay Area have been expanding the scale of their innovation networks, with increasingly close internal and external links and enhanced innovation diffusion capacity. 2) The external links of the innovation network of cities are stronger than internal links, external demand is greater than external supply, and major cities have different internal and external functions in different links of the innovation chain. 3) Spillover capacity of fundamental research and industrial structure similarity have a positive contribution to each link of the city innovation network and its innovation chain. Differences in marketization index and geographical distance show a negative correlation on the impact of each link of innovation, and the gap in economic development level shows a positive correlation in the technology development link and a negative correlation in the industrial transformation link of the enterprise network.Based on the shortcomings and obstacles of the synergistic relationship between urban innovation networks and innovation chains and the differences in their influencing factors, we propose policy recommendations to enhance the synergistic ability of innovation chains with the focus on strengthening and complementing chains.