A smart city provides its people with high standard of living through advanced technologies, and transport is one of the major foci. With the advent of autonomous vehicles (AVs), an AV-based public transportation system has been proposed recently, which is capable of providing new forms of transportation services with high efficiency, high flexibility, and low cost. For the benefit of passengers, multi-tenancy can increase market competition leading to lower service charge and higher quality of service. In this paper, we study the pricing issue of the multi-tenant AV public transportation system and three types of services are defined. The pricing process for each service type is modeled as a combinatorial auction, in which the service providers, as bidders, compete for offering transportation services. The winners of the auction are determined through an integer linear program. To prevent the bidders from raising their bids for higher returns, we propose a strategy-proof Vickrey-Clarke-Groves-based charging mechanism, which can maximize the social welfare, to settle the final charges for the customers. We perform extensive simulations to verify the analytical results and evaluate the performance of the charging mechanism.