It is logical that organizations pay more attention to their major customers which have more impacts on their abilities or benefits. In many real cases, decision makers in scheduling system must prioritize the sequence of processing orders according to the agent of orders while the classic production scheduling do not have the ability to consider the relationships between agents. These problems can be modeled by the Stackelberg problems in the field of game theory. In this study, an agent-based hybrid flow shop problem is formulated by using the multi-leader multi-follower mathematical model. Each level is evaluated by Nash equilibrium and Nash bargaining with the new co-evolutionary and genetic algorithm. The proposed model is validated in a real case problem in the tire manufacturing industry. The results show that Nash equilibrium is superior to Nash bargaining for all agents.