Large-scale Multi-disciplinary Systems(LMS) such as transportation, aerospace, defense etc. are complex systems in which there are many subsystems, interfaces, functions and demanding performance requirements. Because many contractors participate in the development, it is necessary to apply methods of sharing common objectives and communicating design status effectively among all of the stakeholders. The processes and methods of systems engineering which includes system requirement analysis; functional analysis; architecting; system analysis; interface control; and system specification development provide a success-oriented disciplined approach to the project. This paper shows not only the methodology and the results of model-based systems engineering to Automated Guided Transit(AGT) system as one of LMS systems, but also propose the extension of the model-based tool to help manage a project by linking WBS (Work Breakdown Structure), work organization, and PBS (Product Breakdown Structure). In performing the model-based functional analysis, the focus was on the operation concept of an example rail system at the top-level and the propulsion/braking function, a key function of the modern automated rail system. The model-based behavior analysis approach that applies a discrete-event simulation method facilitates the system functional definition and the test and verification activities. The first application of computer-aided tool, RDD-100, in the railway industry demonstrates the capability to model product design knowledge and decisions concerning key issues such as the rationale for architecting the top-level system. The model-based product design knowledge will be essential in integrating the follow-on life-cycle phase activities. production through operation and support, over the life of the AGT system. Additionally, when a new generation train system is required, the reuse of the model-based database can increase the system design productivity and effectiveness significantly.