This paper first applied material flow analysis (MFA) to construct three levels of regional eco-efficiency indicators, i.e., regional direct eco-efficiency (RDE), regional total eco-efficiency (RTE), and holistic eco-efficiency (HE), and adopted the newly developed data envelopment analysis (DEA) to evaluate the eco-efficiency of Tongling City during the period of 1990-2008. We also applied Malmquist productivity index (MPI) to explore the eco-efficiency change between two following years and its driving factors. The main results were summarized as 1) though the RDE of Tongling City in 1990-2008 kept an increasing trend, its mean eco-efficiency was not high (close to 0.8 in 80% of the years), being lower than that of the RTE and HE, and 2) the RDE change was closely relevant to the improvement in resource management and the technical input in environmental protection in recent years. In order to further improve the RDE of the City, it would be necessary to raise its eco-efficiency via expanding raw material input, reducing domestic extraction, promoting resources productivity, and taking more measures on environmental protection facilities construction.