As the microsubjects of transformation and upgrading, enterprises are conducting green innovation to help simultaneously improve economic and environmental quality. However, whether green innovation can promote green total factor productivity (GTFP) remains unclear, especially at a micro level. This study addresses this research gap from an empirical perspective, focusing on Chinese A-share listed enterprises and using economic and environmental statistical data at the province and city levels from 2004 to 2019. Results show that green innovation improves GTFP. The impact of green innovation on GTFP is heterogeneous, depending on patent types and characteristics of enterprises. Additionally, technical gaps influence the impacts of green innovation on enterprise GTFP. It has a threshold effect in heavy-pollution enterprises. Green innovation inhibits enterprise GTFP when the technical gap is less than 132.7233. When the technical gap is more than 142.4535, green innovation promotes the enterprise GTFP. Our research provides microscopic evidence on green transformation for enterprises with heterogeneous characteristics and green innovation.