The world is being reshaped under global economic development driven by new advances in information technology. Artificial intelligence, an essential potential technology, will play a vital role in technological change and industrial upgrades. Exploring the relationship between government subsidies, green innovation, and total factor productivity will help us analyze government decisions’ effects and better promote artificial intelligence’s technological innovation process. Based on data from China’s listed artificial intelligence companies from 2011 to 2020, this study uses the Levinsohn–Petrin method to measure the total factor productivity of companies and analyzes the impact of government subsidies on the total factor productivity of AI companies, the mediating effect of green innovation, and the moderating effect of intellectual property protection intensity. The research results show that (1) government subsidies can promote the total factor productivity of AI enterprises; (2) green innovation capabilities play a mediating role between government subsidies and enterprise total factor productivity, and government subsidies can indirectly promote green innovation to promote the improvement of total factor productivity effectively; (3) in the AI industry, the promotion effect of government subsidies on total factor productivity is more significant among state-owned enterprises, while the impact mechanism of government subsidies on private enterprises is not significant; and (4) the intensity of intellectual property protection has played a positive moderating role in the impact of government subsidies for artificial intelligence enterprises on total factor productivity. However, the current intensity of intellectual property protection remains unable to promote improvements in enterprise total factor productivity by stimulating green innovation. The research results will help us better understand the relationship between government subsidies and the development of corporate economic benefits and promote more scientific and effective government decision-making.