In the context of the One Country–Two Systems policy, Shenzhen and Hong Kong have rapidly grown into a dual-core international metropolis. However, a huge barrier is the commuting cost incurred by the tariff policy, which blocks the road to the high-quality development of the Guangdong–Hong Kong–Macao Greater Bay Area (GBA). Based on traffic accessibility and kernel density analysis of the subway network and points of interest (POIs) of urban functional areas with ArcGIS, this study analyzed the commute time and convenience level of the functional areas in the two separate tariff zones. The traffic (commute) time in 75 min was taken as the turning point of the efficiency of the Shenzhen–Hong Kong connection, and it was found that both the customs clearance time and the accessible areas show the shape of a parabolic function with an upward opening. It was also found that, in Shenzhen and Hong Kong, the commute time in most of the business, commercial, residential, and industrial areas is 60–75 min. In particular, the comfortable range within 45 min was not achieved. It is necessary to further promote the effectiveness of the Shenzhen–Hong Kong customs clearance system and continuously reduce the customs clearance cost so as to promote the integration of Shenzhen and Hong Kong in order to implement the national strategy of “dual circulation” and innovation-driven development and efficiently drive the coordinated construction of the GBA.
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