It is one of the core contents of our government’s economic work to improve and optimize financial structure to promote the degree of financial structure marketization and economic growth.Based on China’s A-share listed companies from 2013 to 2020,we empirically examine the influence of the degree of financial structure marketization on firm’s capital operation in the region.We find that the lower the degree of marketization of financial structure, the greater the possibility of capital operation of listed companies. Further research shows that the excessive debt of the company plays a part of the intermediary effect in the influence of the degree of marketization of the financial structure on the capital operation of the company. That is, the lower the degree of marketization of regional financial structure, the more likely it is to aggravate the degree of excessive debt of the company, the more likely the company is to carry out capital operation. The negative influence of financial structure marketization degree on corporate capital operation is more significant in non-state-owned enterprises, companies with low growth, high management shareholding ratio and low institutional investors shareholding ratio. The decrease of marketization degree of financial structure will intensify the role of company capital operation in increasing agency cost between controlling shareholders and minority shareholders. This study enriches research on financial structure and capital operation, and provides reference for optimizing financial structure and restraining capital operation.