The key to studying urban sustainable development depends on quantifying stores, efficiencies of urban metabolisms and capturing urban metabolisms’ mechanisms. This paper builds up the metabolic emergy account and quantifies some important concepts of emergy stores. Emphasis is placed on the urban metabolic model based on the slack based model (SBM) method to measure urban metabolic efficiencies. Urban metabolic mechanisms are discussed by using the regression method. By integrating these models, this paper analyzes the urban metabolic development in Beijing from 2001 to 2010. We conclude that the metabolic emergy stores of Beijing increased significantly from 2001 to 2010, with the emergy imported accounting for most of the increase. The metabolic efficiencies in Beijing have improved since the 2008 Olympic Games. The population, economic growth, industrial structures, and environmental governance positively affect the overall urban metabolism, while the land expansion, urbanization and environmentally technical levels hinder the improving of urban metabolic efficiencies. The SBM metabolic method and the regression model based on the emergy analysis provide insights into the urban metabolic efficiencies and the mechanism. They can promote to integrate such concepts into their sustainability analyses and policy decisions.