China proposed establishing a carbon emission trading market in its 12th Five-Year Plan to reduce carbon dioxide emissions through market mechanisms, promote the development of science and technology and help China become an environment-friendly country. To examine the impact of carbon emission trading on green technology innovation in Chinese energy enterprises, data from 1993 to 2020 were collected from 494 A-share-listed energy enterprises. Enterprises located in the pilot area of carbon emissions trading were assigned to the treatment group, while those in the non-pilot area were assigned to the control group. The propensity-score-matching method was utilized to match the treatment group with the control group, and the resulting samples were used as the actual sample data. The difference-in-differences method was then employed to assess the net impact of carbon emission trading and investigate its effect on green technology innovation in energy enterprises. This empirical study suggested that carbon emission trading has a positive impact on green technology innovation in energy enterprises, particularly state-owned ones. Larger enterprises are more willing to engage in green technological innovation than small enterprises. Furthermore, when faced with a carbon emission trading system, ‘mature’ companies tend to pay more attention to green technology innovation than younger enterprises do. This study puts forward policy measures for establishing a national-level carbon emission market in China in the future.