The development and implementation of prefabricated buildings has been accelerating rapidly in recent years due to the ongoing revolution in the construction industry. Among different stages and aspects in completing a prefabricated building project, the selection of the prefabricated structural system is a crucial step because it has direct influence on both the cost and usage of the building. This paper proposed a structural system selection model for five commonly used prefabricated buildings structures based on value engineering’s value coefficient analysis ranking which took both life cycle cost coefficient and functional coefficient into consideration. The proposed model aims at providing an innovative approach assisting early decision making on the selection of structural systems for project stakeholders. The case study provided in this paper demonstrated the feasibility and effectiveness of the proposed model. With proper implementation, the proposed approach can also promote the development of prefabricated buildings due to their cost and value advantages.