Reducing the cost of prefabricated building is an effective way to promote its rapid development. The current research mainly focuses on the materialization stage, while there are few studies on the whole life cycle cost of prefabricated building. Therefore, this paper constructs the index system of influencing factors on the cost of prefabricated building from the perspective of the whole life cycle. The objective and subjective weights of each index are calculated by AHP-entropy weight method, then the final weights are obtained by game theory method. Finally, the most important factors affecting the life cycle cost of prefabricated building are evaluated by gray correlation analysis method. The results show that the assembly rate and prefabrication rate, the degree of standardization of design, the number of mold turnover and the utilization rate of mechanical equipment, the level of construction personnel, the engineering visa and the planned management and maintenance are the most important factors affecting the cost of prefabricated buildings. Taking these six factors as the starting point, suggestions for effective cost control are put forward to provide reference for the development of prefabricated buildings.