The Chengdu-Chongqing economic circle, as an important strategic growth pole in China, urgently requires relying on green technology innovation to accelerate high-quality economic development. This paper is based on the municipal-level panel data of the Chengdu-Chongqing economic circle from 2005 to 2020, explores the impact of green technology innovation on high-quality development using the dynamic panel system GMM model, and identifies the energy-saving and emission reduction channels of green innovation. The results show that: green technology innovation significantly contributes to the high-quality economic development of the Chengdu-Chongqing economic circle; the “energy saving effect” is an effective path for the impact of green technology innovation, but the “emission reduction effect” has an obvious masking effect; according to technology heterogeneity and city location heterogeneity, there is a significant promotion effect of green technology innovation in different characteristic cities, but there are obvious differences in the influencing mechanisms. To further accelerate the high-quality development of the Chengdu-Chongqing economic circle, we should strengthen policy support for green technology innovation, promote the coordinated development of green innovation, increase investment in green technology innovation, improve the mechanism of industry-university-research green innovation cooperation, and optimize the evaluation system for energy saving and emission reduction.