In recent years, Anhui Province has experienced rapid economic development, with a sharp increase in the number of listed companies and the emergence of internal control deficiencies. Starting from the two dimensions of the company’s own characteristics and governance structure, this article sorts out six factors that may trigger internal control deficiencies, including the length of listing, the nature of the company, the number of subsidiaries, the proportion of shares held by the largest shareholder, the experience of mergers and acquisitions, and the proportion of independent directors. Subsequently, through logistic regression analysis of the relevant data of small and medium-sized board listed companies in Anhui Province from 2017 to 2021, it was found that companies with longer listing years, more subsidiaries, larger shareholding ratio of the largest shareholder, and lower proportion of independent directors in the board of directors are less likely to have internal control deficiencies. In addition, compared to companies with experience of restructuring and mergers, companies that have not undergone restructuring and mergers are less likely to have internal control deficiencies. This study provides useful reference for small and medium-sized board listed companies to improve their internal control sies