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Against the background of globalization and informatization, innovation is the primary driving force for regional economic and social development. Urban agglomerations are the main body of regional participation in global competition, and promoting the construction of the Guangdong–Hong Kong–Macao Greater Bay Area is an important strategy for China’s regional economic development. Aimed at the differences in location advantages among cities in the Guangdong–Hong Kong–Macao Greater Bay Area, based on the theory of innovation chain, we developed a three-stage model of “knowledge innovation-scientific research innovation-product innovation”. A three-stage DEA model was used to measure the innovation efficiency of cities in the Greater Bay Area at different stages, and two progressive two-dimensional matrices are constructed to locate the innovation development of cities according to the efficiency value. The results show the following: ① The overall innovation efficiency of the Greater Bay Area urban agglomerations gradually decreased in the process from knowledge innovation and scientific research innovation to product innovation, and the innovation efficiency among cities was unbalanced. ② Shenzhen, Guangzhou, and Hong Kong all performed well in the whole innovation stage, while other cities in the Greater Bay Area showed weakness in innovation at different stages. Based on this, this paper puts forward relevant countermeasures and suggestions for promoting and optimizing collaborative innovation in the Greater Bay Area taking into account factor flow, industrial structure, and innovation network of urban agglomerations.

Urban Innovation Efficiency Improvement in the Guangdong–Hong Kong–Macao Greater Bay Area from the Perspective of Innovation Chains