Transportation technology innovation represented by autonomous driving and car networking has promoted the research on the architecture of a new generation of transportation system characterized by autonomous operation and service. Meanwhile, multi-modal transportation, as a comprehensive transportation mode of road, sea, rail and air, is playing an increasingly important role in the integrated transportation system. Based on the development status of multi-modal transport and the application of Autonomous Transportation System (ATS) technology, this paper comprehensively analyzes the service objects, vehicles, infrastructure and network platforms involved in the multi-modal transport process. We identify the common service domains that can describe the multi-modal transport scenarios with ATS characteristics and the basic system functions within each service domain. The logic architecture of autonomous multi-modal transport is established based on functions as nodes, logical data flows as links, and service operation process. Its construction will promote the rationalization and systematic transformation of multi-modal transport system from "passive" to "active".