The emerging digital economy has facilitated the digital transformation of the logistics industry toward a standard and collaborative state. The logistics infrastructure has accordingly attracted much attention as the basis for supporting digital economy implementation. Moreover, the initiatives of regional collaborative development, such as in the Greater Bay Area (GBA) of China, have accelerated the integration of logistics infrastructure and operation-level collaboration. Fortunately, the Cyber-Physical Internet (CPI) has created new opportunities for promoting infrastructure integration through the cyber, physical and internet dimensions. However, regional infrastructure integration in the GBA faces various challenges associated with CPI network operations. Thus, a bottom-up approach is proposed to facilitate logistics infrastructure integration in the CPI environment based on the conceptual fusion of computer networks. Considering the fundamental difference in network fusion and operation mechanisms between CPI and computer networks, a CPI-LI 2 (logistics infrastructure integration) framework is designed as an integrated solution. Finally, a simulation study is conducted using real-life medical logistics data from the GBA to verify the effectiveness of the CPI-LI 2 framework. Experiments show that the framework is well adapted to large-scale logistics networks with dynamically changing links.