Current research on ecological efficiency usually only involves resource consumption or pollution emission rather than the whole process of inputs and outputs. This paper uses the Ecological Footprint (EF) approach to simultaneously quantify the demand for natural resources and the impact on environmental change from economic growth and measures Ecological Total Factor Productivity (EcoTFP) to analyze the regional and phased features of China's economic growth. The study found that the EcoTFP growth rate showed a downward trend and experienced a W-shaped fluctuation, which benefited from the growth of TFP in the early stage and was mainly affected by the growth of ED in the later stage. Beijing and Shanghai have controlled their ED growth on a large scale, leading other regions in EcoTFP growth, while resource-based regions such as Inner Mongolia and Shaanxi have experienced rapid growth in ED, leading to continuous negative growth in EcoTFP. It is also found that there is a β-convergence trend in EcoTFP growth nationally and regionally, but σ-convergence exists only in the eastern region, and the eastern region has the relatively fastest β-convergence trend. In conclusion, China's green transformation has been effective in the eastern regions, and it is imperative to control the growth of ecological occupation in the western regions, which requires strengthening environmental regulation and protecting functional ecological zones while attracting industrial transfers.