Abstract: Taking the panel data of non-financial listed companies in Shanghai and Shenzhen Stock Exchanges from 2013 to 2016 as examples, this paper studies the impact of internal control and governance structure on operating performance and concretely explores the impact under the background of equity heterogeneity. It is found that both internal control and governance structure have a significant positive relationship with operating performance. And further comparative analysis of the relationship between the three factors in state-owned holding companies and private holding companies shows that government structure has a significant relationship with operating performance in listed companies, but there are obvious structural differences. In addition, compared with private holding companies, internal control has a more significant impact on operating performance in state-owned holding companies.