ABSTRACT The various knowledge flows shape and change the regional innovation patterns, which are also influenced by regional conditions. What are the similarities, differences and connections between science and technology linkage, as two different types of knowledge network, deserve to be explored in depth. Drawing on scientific paper co-publications and patent transfer data, we constructed two different types of intercity innovation networks during 2006–2016 in the Guangdong–Hong Kong–Macao Greater Bay Area (GBA), a city region special for its ‘one country, two systems’ structure. After that, we explored the evolutionary characteristics of the networks and further examined the different impacts of multidimensional proximity on scientific collaboration and technology transfer. Our results show that technology transfer is more sensitive to spatial factors, institutional barriers caused by ‘one country, two systems’ is a bigger obstacle to technology transfer between cities, cultural proximity and cognitive proximity have a more significant impact on paper cooperation network. Moreover, geographical proximity can indirectly affect knowledge spillover by acting on the proximity of other dimensions. As for scientific collaboration, social, cognitive and institutional proximities can compensate for the lack of geographical proximity, and cultural proximity frequently goes along with geographical proximity; as for technology transfer, geographical proximity has neither substitutional or complementarity relations with cultural and cognitive proximities, the interrelatedness between geographical and institutional and social proximities are complementarity which is opposed to paper co-publications. This study explores the differences in spillover mechanisms of different knowledge types and contributes to enriching the empirical framework of multidimensional proximities and innovation network researches.