As for whether the customer risk leads to the inefficient investment of suppliers, 776 suppliers and customers of Shanghai and Shenzhen A-shares from 2007 to 2017 are chosen as the supply chain data of listed companies, the relationship between customer risk and supplier enterprise investment efficiency is studied by manual sorting, and the moderating effect of the nature of supply chain relationship on customer risk and enterprise investment efficiency is taken into account. According to the research, the customer risk will reduce the investment efficiency of supplier enterprises, which is manifested as underinvestment. Based on further research, the relationship is more significant in supplier enterprises with a higher customer concentration and state-owned enterprises that are customers and suppliers. The research of this paper enriches the relevant literature on investment efficiency and the relationship between customer and supplier, provides a new perspective for studying investment efficiency and the empirical evidence for risk prevention behavior among enterprises, and has important practical significance for supplier enterprises to choose core customers and manage customer relations.