Low-altitude air transportation system is a typical system of systems(SoS) which presents a complex challenge in collaborative evolution of advanced air mobility vehicle technologies and integrated operation of unmanned and manned vehicles in a high density airspace. Low-altitude air transportation includes multiple operating scenarios covering emergency service, cargo and passenger transport with high safety and reliable requirements. Stakeholders and heterogeneous air mobility vehicles require interoperability and interactive collaboration to support SoS ecosystem continuous evolution. The emerging low-altitude air mobility vehicles must coexist and collaborate with current air transportation system, and conform to existing airspace management regulations[1]. The low-altitude air transportation SoS design requires an architecture to provide holistic view and comprehensive understanding of the relationship and interactions between constituent systems. In this paper, a low-altitude air transportation system architecture is proposed based on unified architecture framework (UAF). The framework implements a standardized multi-perspective and hierarchical design method to integrate multiple concerns from strategic vision to technical implementations[2]. This paper defines the SoS vision and strategic phases from trial experimentation to business fleet operation. Unmanned cargo and urban passenger transport scenarios are analysed and key capabilities are identified to direct air mobility vehicle system requirement development. The paper defines the SoS operational architecture and analyses low-altitude operation process with information exchange interactions between air vehicle, vertiport, remote pilot and other operational roles. A trade-off analysis is performed between different physical solution architectures to support vehicle system configuration selection.