Enhancing the resilience of industrial and supply chains is a crucial aspect of constructing a new development paradigm. Against the backdrop of increasing supply chain instability, how auditors identify and respond to the risks arising from changes in a firm’s supplier structure is an important issue worth studying. This paper examines this issue from the perspective of audit fees. The study finds that the greater the changes in a firm’s supplier structure, the higher the audit fees. Mechanism testing reveals that significant changes in the supplier structure lead auditors to perceive stronger earnings management motives and higher operational risks in the firm, prompting them to invest more efforts, which in turn increases audit fees. Heterogeneity analysis shows that the positive correlation between supplier structure changes and audit fees is more pronounced when the accounting firm is larger, the rationality of changes in the supplier structure is lower, and the firm receives higher media attention. Furthermore, higher audit fees reduce information asymmetry between the firm and various stakeholders due to significant changes in the supplier structure, thereby lowering stock price synchronicity and alleviating investors’ negative sentiment. In conclusion, this paper shows that auditors increase audit fees to address the risks arising from changes in the supplier structure. From a supply chain perspective, it provides new empirical evidence on audit pricing mechanisms and enriches the literature on the economic consequences of auditing.