Lowballing has led to reduced audit fees, insufficient audit input, and declining audit quality, making audit fee assurance a key regulatory concern. Using Shanghai and Shenzhen A-share listed companies from 2016 to 2022 as samples, this paper examines how IPO audit experience under the registration system affects audit firms’ fees and its mechanisms through multi-period DID analysis. Results show that registration system experience significantly increases audit fees for firms auditing companies under the approval system, with legal risk awareness and audit input as key channels. The impact is greater when signing CPAs have higher ranks, registration system business is larger, and client importance is higher. Policymakers should enhance legal frameworks, encourage participation in registration system IPO audits, and promote related cultural development to support organizational transformation.