Green development answers to the common needs and demands of all humanity, especially the emerging economies like China. Based on the newly constructed Metafrontier-Global-SBM super-efficiency DEA (Data Envelopment Analysis) model, this study measures the green economic growth levels of 286 prefecture-level cities in China from 2003 to 2018 and examines their spatiotemporal evolution characteristics and internal influencing mechanisms. The empirical findings highlight that China achieved favorable green economic growth with the most significant improvement in the northeast and eastern coastal cities. In terms of regional distribution, green economic growth in Shanghai, Guangdong, Heilongjiang, Gansu, and Ningxia was at a higher level, while the Chongqing and Qinghai regions were lagging. Based on the decomposition results of the green economic growth rate; the study argues that “innovation effect” was the primary factor driving growth and “technology-leader-transfer effect” showed a contrary inhibiting effect. This study adds empirical evidence to the facts of green development in Chinese cities and the influencing mechanisms behind it, and has important policy implications for further harmonizing the relationship between resource conservation, environmental protection and economic development, and further promoting green development in China and globally.