With the rapid development of intelligent transportation systems, Beidou-based free-flow toll collection technology has become an important research direction to improve road traffic efficiency and toll management level. Addressing issues such as the ambiguity of routes and large trajectory deviations caused by inaccurate positioning results in the current Beidou Free-Flow tolling, which mostly adopts a holistic pricing approach, this paper proposes a Beidou Free-Flow tolling technology based on segmented pricing and designs a corresponding Beidou Free-Flow tolling system. Through real-road tests, the Beidou free-flow toll collection technology based on segmented billing proposed in this paper reduces construction costs and decreases the difficulty of auditing, while ensuring the accuracy and reliability of billing. At the same time, this technology also has good scalability and compatibility, which can provide strong support for the construction of future intelligent transportation systems.