In regions where transportation and the economy are closely integrated, optimizing network structure and enhancing synergy are vital for regional integration. This paper constructs a dual-factor linkage network using enterprise investment and liner shipping data to analyze linkage strength and synergy effects among cities in the Greater Bay Area. The findings reveal that (1) a core-periphery structure exists, with core cities dominating resource flows while secondary cities remain weak. The logistics network is led by Hong Kong and Shenzhen, while the capital flow network showcases the dominance of Hong Kong, Shenzhen, and Guangzhou. (2) From 2016 to 2021, interactions between transportation and the economy deepened, showing strong correlations in logistics and capital flows among core cities and between core and edge cities, but weaker correlations with sub-core and edge cities. Core cities stabilize regional transportation and economy, fostering agglomeration, while sub-core cities are more reliant on them, indicating a need for better resource balance. (3) The spatio-temporal coupling analysis reveals significant heterogeneity in flows among cities, with many exhibiting antagonistic couplings outside core areas. This study enhances understanding of synergy mechanisms in transportation and economic networks, offering insights for optimizing layouts and improving capital flow efficiency.