Based on the existing mode of the supply chain of imported bonded commodities for cross-border e-commerce enterprises, this paper studies and discusses the online operation method of bonded commodities, warehousing management, logistics and transportation, as well as consumer satisfaction, and draws on the operation mode of the supply chain of domestic general trade goods, and tries to make innovations to the operation and management of the whole cross-border bonded commodities supply chain based on this model. The authors of this paper found that updating the sales strategy and cooperation between the supply chain could help merchants accurately predict the positioning of commodities and market demand, which is helpful for cross-border e-commerce enterprises to grasp the market trends and consumption trends and avoid the inventory backlog in bonded warehouses. In addition, the innovation of bonded merchandise sales could increase the consumer attention of different groups of consumers, accelerate the circulation of goods and increase the sales of goods. It helps cross-border e-commerce enterprises to enhance their market competitiveness. Finally, merchants, through the management of logistics and transportation, through cooperation and data sharing, can better reduce logistics and transportation costs and rapid delivery.