In the face of the increasing number of enterprises without actual controllers, how auditors view this special governance structure needs to be empirically tested. Taking Shanghai and Shenzhen A-share listed companies from 2011 to 2024 as research samples, this paper discusses the relationship between the absence of actual controllers and going-concern audit opinions. The study found that companies without actual controllers are more likely to be issued a going concern audit opinion. Further distinguishing the types of opinions, it is found that such enterprises are more likely to be issued to continue operations and cannot express opinions. The mechanism test shows that the absence of actual controllers increases the business risk and litigation risk of the enterprise, which in turn leads to an increase in the probability of being issued a going concern audit opinion. Heterogeneity analysis reveals that when auditors have rich experience, investors pay more attention, the quality of information disclosure is poor, and the quality of internal control is low, companies without actual controllers are more likely to be issued a going concern audit opinion. After testing, the auditor issued a going concern audit opinion for the sake of maintaining reputation capital and avoiding regulatory risks, and the motivation was verified. The research conclusions have important implications for understanding the auditor’s risk decision-making mechanism and improving corporate governance.