Limited by traditional construction project management ideas and systems, the implementation of the PMC model in China still has serious problems such as opposition and frequent conflicts. How to reveal the causes of organizational conflicts and explore the key mechanism of the implementation of the PMC model from the system perspective are urgent problems to be solved. Based on the idea of engineering system view, this paper abstracts the PMC project participants with self-organizing characteristics of the organizational management system, in which the internal structure is closely related, and defines the connotation of synergy and synergistic evolution of the PMC project organizational management system. Using the Cucker–Smale model to describe the group movement, the hierarchical system and the acceleration efficiency function of the project legal person’s free will are constructed, and the structure, movement, and development law of the system itself are emphasized to simulate the ordered evolution trend of PMC project organizational management system and reveal the intrinsic causes of conflicts in PMC project and the key mechanisms of the PMC model application. The results show that first, the intensity of information communication between PMC subjects has a significant positive contribution to the orderliness of the organizational management system; second, too much acceleration of the project legal person’s free will causes group chaos in the system, while too little slows down the group stabilization time, which has a negative impact on cost and schedule; third, the more the organizational structure of PMC contractors tends to the whole-process integrated control, the more it can drive the group to gather in an orderly manner and form a synergistic control mode combining self-organization and other organizations; and fourth, the implementation of the PMC model should focus on eliminating the traditional institutional and conceptual barriers, forming a project management model with integrated control of the whole process of the PMC project contractor and effective macro supervision of the project legal person. The research results of this paper revealed the intrinsic causes of conflicts in PMC projects and the key mechanisms of PMC model application; it can help solve the confrontational situation of PMC project participants, promote the development of the PMC model, and give full play to the investment benefits.