As a main new business model of Internet plus foreign trade, cross-border e-commerce has become an important way and breakthrough for China creating new foreign trade requirements in Internet economy. Cross-border supply chain management is one of the most important supports for cross-border e-commerce. Compared with domestic e-commerce, the supply chain of cross-border e-commerce faces more risks. In order to effectively identify and avoid the operational risks in the cross-border e-commerce supply chain, this article firstly analyzes the cross-border e-commerce supply chain risks from the operation process of the cross-border e-commerce supply chain. The risks include product selection management risks, cross-border transaction risks, and customs clearance risks that exist in the operation of cross-border e-commerce. Secondly, the cross-border e-commerce supply chain risk evaluation index system is established based on the risk elements. Finally, the risk evaluation is carried out through the FUZZY-ISM evaluation method, and the internal connection of each risk factor and the risk generation mechanism are revealed through structural model analysis, which provides a theoretical reference for cross-border e-commerce enterprise supply chain risk management.