In order to explore the impact of high-tech industrial clusters and cluster models on green innovation efficiency, this paper based on China’s provincial panel data from 2008 to 2018, using GML index to measure the green innovation efficiency including unexpected output. Constructing panel regression and threshold econometric models between high-tech industry agglomeration and green innovation efficiency to investigate the impact of different agglomeration high-tech industry on green innovation efficiency. The results show that: there is an inverted U-shaped relationship between high-tech industrial agglomeration and green innovation efficiency. There is a nonlinear relationship between specialized agglomeration and green innovation efficiency. There is a positive linear relationship between diversified agglomeration and green innovation efficiency. The above three results mean that scientific high-tech industrial agglomeration mode and appropriate agglomeration degree can effectively improve green innovation efficiency.