Over the past forty years of reform and opening up, the urban center system in the Pearl River Delta Region has been rapidly restructured. Its two central cities, Guangzhou and Shenzhen, have been fiercely competing in the field of economic development. Dealing with the functional positioning of the two cities has constituted a long-term concern for regional planning and policy making. Under the new circumstances of the Guangdong-Hong Kong-Macao Greater Bay Area, there is an urgent need to clarify the functional positioning of the two central cities of Guangzhou and Shenzhen. Further, there is a need to coordinate the relationship between competition and cooperation, the premise of which lies in the dynamic and accurate identification of urban functional characteristics. Previous studies directly used economic and industrial statistical data to study and analyze urban functions. However, due to the relative low frequency and high cost of data collection and analysis, it is difficult to carry out real-time analysis using these data. Based on the theoretical understanding of the projection of city functions to the city network, this article uses inter-city air passenger flow as its research medium. Further, it uses the air passenger flow data extracted from Baidu location-based services (LBS) big data. Taking the Chinese city network as its overall scope, it adopts the following two approaches. First, it compares the functional characteristics of the cities where the air passenger flows toward Guangzhou and Shenzhen are sourced. Second, it compares the functional characteristics of the employment places in the two megacities of Beijing and Shanghai, where the air passenger flows toward Guangzhou and Shenzhen are sourced. Therefore, the functional attributes and the functional areas of the source cities are used as the basis for identifying the comparative functional features of Guangzhou and Shenzhen to judge their overall functional characteristics in the Chinese urban network. The research results show the following. 1) First, compared with Shenzhen, Guangzhou's network connection with cities across China and Beijing and Shanghai focuses on administrative management and business functions. It plays the role of an administrative and business center within the spatial scale of the Pearl River Delta urban agglomeration. 2) Second, compared with Guangzhou, Shenzhen focuses on technological innovation, finance, and high-tech manufacturing functions, and plays the role of a technological innovation and financial center and high-tech manufacturing base under the scale of the Pearl River Delta. 3) Third, as the two major service industry centers in the Pearl River Delta region, Guangzhou focuses on public and general producer services, and Shenzhen focuses on advanced producer services such as finance and technological research and development. Shenzhen has a higher status within the Chinese urban network system based on the producer service industry. The method provided by this article, which involves locational big data to flexibly extract urban functional characteristics from the city network, is novel. Further, it can serve as a supplementary approach to the studies on urban functions which relied on traditional economic and industrial statistics. Meanwhile, the research results of this article provide evidence for deepening the theoretical understanding of the urban function-space-network mapping relationship.