Abstract:The research on innovative collaborative mechanism in Guangdong-Hong Kong-Macao is a hot topic, but there are still some gaps in the research on the collaborative mechanism of basic research in the Greater Bay Area(GBA).This paper is based on the basic research resources endowment of GBA to establish the cost coordination model of collaborative innovation.According to game analysis by Rubinstein game model, we found that sharing the R&D cost and sharing the benefit of research is the best way of collaborative innovation between enterprise and university. Based on this, we constructs a conceptual model of "target synergy - process synergy - resource synergy - results synergy" for basic research in GBA. At last, we put forward policy advices according to the conclusion.