Quality of agricultural products catches the eye of the public. This paper considers two levels of supply chain including a supplier and a retailer to establish two kinds of differential game models: Stackelberg game model led by retailers and the game model under subject cooperation. Optimal quality effort level is considered as state variable and optimization decision of supplier and retailer can be solved using the method of feedback. The results show that under certain conditions subject cooperation can achieve Pareto improvement of suppliers, retailers and the entire supply chain system profit. The conditions of achieving Pareto are analyzed to promote the coordination of the fresh agricultural product supply chain on the basis of above research.