Prefabricated buildings have advantages such as energy conservation and high efficiency, but the problem of high costs hinders their rapid development. Insufficient collaboration among participants and an imperfect policy system have led to increased costs of prefabricated buildings. From the perspective of transaction costs, this paper establishes an indicator system affecting the transaction costs of prefabricated buildings based on the WSR methodology, and identifies 31 influencing factors through literature review. AMOS software is used to conduct reliability and validity tests, confirmatory factor analysis, and path test analysis on the collected questionnaires to verify the fitness between the theory and hypotheses. The SEM analysis results show that factors such as project characteristics, market environment, decision management, contract management, construction management, personal systems, and enterprise systems have a negative impact on the transaction costs of prefabricated building projects. The model results can provide reference for general contracting enterprises to reduce the transaction costs of prefabricated buildings.