Corporate governance is the top design of internal control. The change of “double no control”, which has neither actual controller nor controlling shareholder, will inevitably affect the quality of internal control. Therefore, we choose A-share listed companies in Shenzhen and Shanghai Stock Markets from 2009 to 2019 as the research sample to test the influence of double no control on the major defects of internal control of listed companies. It is found that compared with other companies, double no control companies have a higher probability of major internal control defects, in which the first type of agency problem plays a partial intermediary role. The heterogeneity test shows that when the total remuneration of company executives is higher, the proportion of male executives is higher, the average age of executives is smaller, and the scale of company supervisory board is smaller, and the shareholding ratio of institutional investors is lower, the influence of double no control on major internal control defects is greater. Further research shows that in the “double no control” enterprises where the top ten shareholders are related or belong to the concerted action, two kinds of agency problems coexist, and lead to serious defects of internal control. The conclusion not only expands the perspective of internal control, but also provides empirical evidence and policy reference for perfecting internal governance mechanism and improving the quality of listed companies.