In the process of meeting the transportation needs of people and goods, emerging technologies make the transportation system change from “passive” to “active”, which gives birth to the concept of autonomous transportation system. The boundary of traditional transportation system architecture is relatively fixed, and the internal data utilization rate of the system is low. It is no longer suitable for the transportation industry under the application of emerging technologies, and its construction idea is also hard to guide the construction of ATS system. System engineering is a methodology to guide system analysis and construction, which is widely used in system construction. Based on the method of system engineering, this paper first compares and analyzes the application of process-oriented and object-oriented in architecture design. On this basis, it is proposed to divide the architecture construction of ATS into two stages: demand analysis and architecture design. In the demand analysis stage, five elements of ATS technology, demand, service, function and composition are determined from the following steps: system boundary division, determination of influencing factors and mechanisms, refinement of service implementation process and hardware research. In the architecture design stage, according to the characteristics of ATS services, the functional, logical and physical architecture of each service is designed, and finally the analysis of ATS based on system engineering methodology is completed.