Green technology innovation is an important driving force for low-carbon development of enterprises. As a market-based environmental policy to promote greenhouse gas emission reduction, whether carbon emission trading scheme (ETS) can encourage enterprises to carry out green technology innovation under the background of “dual carbon” goal deserves further research. Taking Chinese A-share listed enterprises in the five major sectors as samples, this study constructed a modified Difference-in-Differences (DID) model to test the causal effect of ETS on green innovation in high-carbon industries. Three significant results can be summarized from the empirical study. Firstly, the ETS has a significant promoting effect on green innovation of high-carbon enterprises. And it can effectively promote high-carbon enterprises to achieve an average of a 13.24–19.56% increase in low-carbon innovation capabilities. Secondly, enterprises with different characteristics have heterogeneity in the impact of ETS implementation on green innovation. Secondly, the implementation of ETS exerts heterogeneous effects on green technology innovation across enterprises that possess diverse characteristics. Enterprises with a large capital scale (low equity concentration) have a more significant promoting effect than those with a small capital scale (high equity concentration). Thirdly, the green innovation effect of ETS exhibits significant heterogeneity across different types of industries. In the mining, manufacturing, and construction sectors, the ETS has effectively stimulated green innovation to a certain extent. There has been no significant change in green innovation in the sector of electricity, heat, gas, and water production and supply. In particular, after the implementation of the ETS, green innovation has actually been weakened in the transportation sector. As such, for policy makers, differentiated ETS policies should be implemented based on the actual situation of different industries and types of carbon-emitting enterprises.