The improvement of green innovation efficiency of high-tech industry is of great significance to promote the high-quality development of China's economy. In order to discuss the impact of government subsidies mode on the green innovation efficiency of high-tech industry, super-SBM model was used to calculate the green innovation efficiency of high-tech industry, and panel regression model was used to empirically analyze the role of government R&D subsidies and tax incentives in this paper. The results show that the overall trend is gradually decreasing from east to west. From a national perspective, both government R&D subsidies and tax incentives can improve the efficiency of green innovation. From a regional perspective, government R&D subsidies are negatively correlated with the efficiency of green innovation in the eastern and central regions, and positively correlated with the western region; tax preference is positively related to the efficiency of green innovation in various regions. Therefore, government departments should formulate differentiated support policies, increase tax incentives for core technology R&D, and optimize the external environment to further promote the efficiency of green innovation in high-tech industries.