Against the background of carbon peaking and carbon neutralization, green technology innovation plays an important role in promoting the energy total factor productivity (TFP). This study verifies the impact of green technology innovation on energy TFP in a complete sample and the subsamples by region, by constructing a panel threshold model, and analyzes its influence mechanism on the basis of the mediating effect test based on annual provincial data of mainland China from 2005 to 2018. The empirical results reveal the following: first, with the level of economic development as the threshold variable, there is a threshold effect in the impact of green technology innovation on the energy TFP; second, green technology innovation has an impact on the energy TFP through industrial structure upgrading; that is, industrial structure has a mediating effect in the influence mechanism; and third, there is heterogeneity in the impact of green technology innovation on the energy TFP among different regions in China, and the threshold effect only exists in the western region, since the central and eastern regions have crossed a certain developmental stage.