In this paper, the collaborative knowledge innovation network was constructed by using the co-authored papers of Guangdong-Hong Kong-Macao greater bay area (GBA)urban agglomeration (11 cities in the Guangdong-Hong Kong-Macao greater bay area and 6 surrounding) cities from 2008 to 2018 in the core collection database of Web of science. Further, using social network analysis method, this paper studies the structure and evolution of collaborative knowledge innovation network in GBA urban agglomeration, and investigates the influencing factors of the collaborative knowledge innovation network by QAP regression method. On the basis of above researches, major conclusions can be drawn as follows:The collaborative knowledge innovation network of GBA urban agglomeration achieves full coverage in the region with high network accessibility but six cities around the Pearl River Delta are still marginal in GBA urban agglomeration showing a multicenter trend gradually； With the evolution of time, the effects and degrees of different factors on collaborative innovation are different. The influence of Internet accessibility is more and more important, and the influence of cognitive distance is gradually weakening.