To achieve the harmonious development of economic growth and the environment, nations must pay more attention to wastewater treatment and boost efficiency using green technology. This study applies the Malmquist-DEA model to assess the efficiency of green technology innovation in 19 Chinese wastewater treatment companies between 2017 and 2020. In addition, focus is placed on the core wastewater treatment technology of the companies with excellent performance, indicating how wastewater treatment companies may improve their green technology. The results of the study indicate that, first, the overall effectiveness of green technology innovation in companies follows a rising and then decreasing trend. In 2020, wastewater treatment companies’ green technology innovation efficiency was around 17.4 percent lower than in 2017. Improving technical progress is the key to boosting the total factor productivity of wastewater treatment companies. Second, based on the Tobit regression, the shareholding ratio of companies has a positive influence on the technical efficiency of companies. Therefore, China should increase innovation capacity and productivity, adopt current sewage treatment technology from overseas, and thus gradually achieve clean sewage utilization and ecological environment management.