Green technology innovation (GTI) is an important carrier to promote green development, and improving the resources allocation efficiency of GTI is an important way to accelerate the realization of green development. This paper evaluates the resources allocation efficiency of GTI in provinces (municipalities and autonomous regions) of China based on the SBM model of non-expected output super-efficiency, and combines the Meta-frontier Malmquist index analysis to analyze the dynamic change of innovation resource allocation efficiency from 2010 to 2020 from the perspective of regional technology differences. The results show that the resources allocation efficiency of GTI in China has a change trend of first rising slowly and then decreasing slowly, and there is still a large room for improvement. At the same time, due to the influence of regional technology differences, the resources allocation efficiency of GTI in eastern, central and western of China shows different advantages and disadvantages. Based on this, the paper finally puts forward corresponding policy suggestions for the east, central and western regions from the aspects of policy formulation, resource investment and talent introduction.