Mobility as a Service (MaaS) is a smart mobility model that integrates mobility services to deliver transportation needs through a single interface, offering users flexible and personalizd mobility. This paper presents a structural approach for developing a MaaS system architecture under Autonomous Transportation Systems (ATS), which is a new transition from the Intelligent Transportation Systems (ITS) with emerging technologies. Five primary components, including system elements, user needs, services, functions, and technologies, are defined to represent the system architecture. Based on the components, we introduce three architecture elements: functional architecture, logical architecture and physical architecture. Furthermore, this paper presents an evaluation process, links the architecture elements during the process and develops a three-layer structure for system performance evaluation. The proposed MaaS system architecture design can help the administration make services planning and implement planned services in an organized way, and support further technical deployment of mobility services.