In order to have a comprehensive eco-efficiency measure which can incorporate productivity, resource efficiency, environmental efficiency, and inter-temporal comparability and circularity, the paper proposes an extended data envelopment analysis model, named GB-US-SBM model, which combines global benchmark technology, undesirable output, super efficiency and slacks-based measure. Using the GB-US-SBM model, this paper investigates the dynamics of regional eco-efficiency in China from 2000 to 2010. The empirical results show that the movement of average eco-efficiency of China presents a “V” shape from 2000 to 2010 with the trough occurred in 2005, but there are big differences of eco-efficiency among the regions. For the growth of eco-efficiency, technological progress contributes 56.87%, 58.21%, 18.27%, 62.19%; scale efficiency contributes 40.01%, 61.14%, 167.43%, 39.12%; efficiency change contributes 3.82%, −19.99%, −63.40%, −2.16% to the eastern, middle, western and northeastern regions of China respectively. These imply that there is a big space for western region to enhance its technological progress, and huge space for the whole country to promote its management ability.