The driving force of new quality productivity comes from innovation, and breakthrough green technology innovation is its important engine. Breakthrough green technology innovation is the core driver of new quality productivity, and it is an important support to promote and develop new quality productivity. Based on the panel random effect model, the model of regional carbon emission impact on breakthrough green technology innovation is tested, and the mediating effect model is used to explore the impact and path of carbon emission on breakthrough green technology innovation. Heterogeneity analysis shows that in the eastern, northeastern and western regions, carbon emissions significantly inhibit breakthrough green technology innovation. While in the central region, the effect is not significant. In addition, it was found that R&D capital investment partially mediated between carbon emissions and breakthrough green technology innovation, and the number of R&D staff investment mediated insignificantly between carbon emissions and breakthrough green technology innovation. Finally, recommendations are made at the levels of policy, enterprises, collaboration among research subjects, and regional development.