Input-output analysis has been proven to be a powerful instrument for estimating embodied (direct plus indirect) energy usage through economic sectors. Using 9 economic input-output tables of years 1987, 1990, 1992, 1995, 1997, 2000, 2002, 2005, and 2007, this paper analyzes energy flows for the entire city of Beijing and its 30 economic sectors, respectively. Results show that the embodied energy consumption of Beijing increased from 38.85 million tonnes of coal equivalent (Mtce) to 206.2 Mtce over the past twenty years of rapid urbanization; the share of indirect energy consumption in total energy consumption increased from 48% to 76%, suggesting the transition of Beijing from a production-based and manufacturing-dominated economy to a consumption-based and service-dominated economy. Real estate development has shown to be a major driving factor of the growth in indirect energy consumption. The boom and bust of construction activities have been strongly correlated with the increase and decrease of system-side indirect energy consumption. Traditional heavy industries remain the most energy-intensive sectors in the economy. However, the transportation and service sectors have contributed most to the rapid increase in overall energy consumption. The analyses in this paper demonstrate that a system-wide approach such as that based on input-output model can be a useful tool for robust energy policy making.