The green innovation strategy has gradually become the key for enterprises as microeconomic entities to gain competitive advantages and adapt to complex changes in the external environment. Using the data of A-share listed companies in Shanghai and Shenzhen from 2010 to 2020, this paper empirically explores the impact and specific mechanism of the ownership structure of multiple major shareholders on the green innovation of enterprises. The results show that, compared with the shareholding structure of a single major shareholder, a publicly traded company with a multi-stakeholder ownership structure has a higher level of green innovation. The mechanism test shows that the equity arrangement of multiple major shareholders promotes green innovation by alleviating the fluctuation in the cash flow of the enterprise. This paper further examines the effect of regulation of multiple major shareholders on corporate green innovation and finds that green finance and the protection of intellectual property can form an effective complementary mechanism with the equity arrangement of multiple major shareholders, thereby strengthening the green innovation of enterprises. After the robustness test is carried out by the double-difference method, the two-stage instrumental variable method, and the substitution variable method, the empirical results of this paper are still valid.