In the face of resource and environmental problems caused by extensive economic development, China has put forward a green development strategy. Scientific measurement and analysis of green total factor productivity (GTFP) is of great significance for achieving high-quality economic development. By introducing the human capital composition, including education, health, scientific research, and training, this paper study adopts the Slack Based Measure-Global Malmquist-Luenberger (SBM-GML) index to re-measure the GTFP and its decomposition of 30 provinces, municipalities, and autonomous regions in China from 2000 to 2019. The results show that: (1) China’s GTFP has a fluctuating growth trend, with an average annual growth rate of 2.31%. (2) In terms of its decomposition, technical progress is the main force driving GTFP growth, with a contribution rate of 1.59%; the improvement of technical efficiency is a secondary driving force, with a contribution rate of 0.71%. (3) The measurement results of GTFP, considering the human capital composition, are generally higher than those without consideration, and the GTFP growth under the two modes shows a trend of “high in the east and low in the west”. The conclusions have enlightening significance for improving GTFP and the growth potential of the economy in China.