The Guangdong-Hong Kong-Macao Greater Bay Area (GGBA) is a cross-border global city region with Chinese characteristics. However, due to data acquisition limitations, most of the research has focused on the analysis of the spatial pattern evolution of the 9 cities in the Pearl River Delta of the Chinese mainland or mainly on Hong Kong, Macao and inland cities alone. As for cross-border economic relations, port research mostly focuses on the spatio-temporal distribution pattern and mechanism of the port itself, while it rarely involves the spatial linkages and impact analysis of the port on the entire cross-border region. This paper attempts to understand the spatial linkages of China′s cross-border global city regions from the perspective of port linkages. Taking 11 cities of the GGBA as an example, this study applies analytical methods including port linkage strength, network density and Python programming. Moreover, this research views the sea, land and air cross-border ports as nodes and takes the port traffic linkages as links to analyze the impact of ports on the spatial linkages of the Bay Area. The results show that: (1) ports are an important channel for the internal spatial connections of the cross-border global city region of ??the GGBA. Relying on each port, the Bay Area has formed a macro-linkage pattern with Hong Kong as the core and Macao, Shenzhen and Guangzhou as important nodes. (2) The sea port connection is manifested as a linkage pattern led by Hong Kong as the core with interactions between Hong Kong and Macao, while the sea ports connection between Hong Kong, Macao and other cities in the Bay Area shows hierarchical differences. (3) The land port connection indicates that the Bay Area has formed a radial linkage pattern with the Hong Kong and Macao land ports as the origin, and the Pearl River is the boundary demonstrating a significant imbalance. (4) The air port connection presents a linear and radial outreach pattern with Hong Kong and Macao as the core and facing the GGBA. This paper reveals the impact of port linkages on the spatial linkages of global city regions as well as the flow of factors in the cross-border areas, and thus provides a new perspective for the study of cross-border regional linkages.