With the continuous development of global supply chain, stable supply chain relationship becomes more and more important. This paper discussed whether and how the change of customer relationship affects audit fees from the perspective of auditor risk response. The empirical results showed that the change of customer relationship significantly increases audit fees. The mechanism test showed that the change of customer relationship makes auditors increase audit input and perceive higher audit risk, and then charge higher audit fees. After further exploring the causes of customer relationship changes and their impact on audit fees, it is found that auditors charge higher audit fees when customers themselves face financial difficulties. However, when the economic policy uncertainty is high, the customer relationship changes will be reduced, thus reducing audit fees. The heterogeneity test at accounting firm level and firm level also showed that the positive relationship between customer relationship changes and audit fees is mainly reflected in the "Top10" domestic accounting firms, enterprises with high customer concentration and low governance level. This study provided new evidence and perspectives for discussing the economic consequences of customer relationship changes, and had enlightening significance for the current supply chain risk management in China.