How to promote corporate green innovation while alleviating the high financing cost of enterprises is an urgent problem to be solved at present. Based on the data of China’s GEM listed companies from 2009 to 2022, this paper uses the fixed effect model and the mediating effect model to study the impact and mechanism of enterprises green innovation capability on debt financing cost and equity financing cost. The results show that the green innovation ability of GEM listed companies can significantly reduce their own debt financing costs and equity financing costs, and enterprise performance and market attention are the main influence paths of green innovation capability. In addition, the green innovation capability of enterprises is more significant in reducing the financing cost of non-state-owned enterprises, manufacturing industries and enterprises with environmental information disclosure. Therefore, enterprises should further improve the level of green innovation, and at the same time, the government further increases the support for enterprises green innovation to provide a relaxed environment for enterprises green innovation.