Improving eco-efficiency to coordinate the relationship between economic development and environmental protection is very important. This study, based on the input-output table for Beijing, used the index system method to increase understanding about the eco-efficiency of various sectors currently undergoing industrial transformation and identify the key to improving eco-efficiency. Water resources, waste water, sulfur dioxide, and industrial solid waste were analyzed to create the index of eco-efficiency. They were used to assess the resource efficiency of the water resources in 2007, 2010, and 2012 for Beijing, as well as the environmental efficiency of each sector in 2005, 2007, and 2010. Then this study compared the complete water use coefficient and pollutant total discharge coefficient, calculated the total emissions contributions made by different sectors, and identified key ways to improve the efficiency of the ecological sector. The main conclusions are as follows:(1) the water efficiency between 2007 and 2012, and the environmental efficiency of wastewater, SO₂, and industrial solid waste for each sector in Beijing between 2005-2010 increased, but this increase was variable; (2) the agriculture, livestock, forestry, fishery, and the waste material industries are key sectors that have a role in improving water efficiency; (3) water production and supply, the chemical industry, food manufacturing and tobacco processing, textiles and paper printing, and the cultural and educational sporting goods manufacturing industry are the key sectors that have most effect on improving the environmental efficiency of waste water; (4) petroleum processing, coking and nuclear fuel processing, non-metallic mineral products, the metal smelting and rolling industry, and the electricity, heat production and supply industry are the key sectors that have most effect on improving SO₂ environmental efficiency; and (5) the coal mining and washing industry, metal mining, wood processing and furniture manufacturing, non-metallic mineral products industry, metal smelting and rolling, electricity, heat production and supply industry, and the water production and supply industry are the key sectors that can help improve industrial solid waste efficiency.