In contrast to measuring the end energy consumption, the embodied energy analysis could provide systematic accounting of regional energy system with regard to direct and indirect terms. Presented in this paper is an embodiment analysis of urban energy system of Beijing during the period of 1987-2007 using input-output technique. Results show the energy consumption in Beijing increased rapidly during 1987-2007: direct energy consumption increased from 20.03 to 52.80 Mtce while the embodied energy consumption increased from 38.86 to 206.20 Mtce; Meanwhile, the energy intensity presents a declined trend but the decrease of energy intensity slows down especially during the last five years; The proportion of direct energy decreased from 51.55% to 25.60% while that of the indirect energy grow from 48.45% to 74.4% among embodied energy of Beijing; The primary sectors of energy consumption are transforming from the traditional heavy industry to modern manufacture, construction and the tertiary sector with relatively low direct energy consumption but higher indirect consumption; The evident contrast between direct and indirect energy consumption demonstrated the fact that the traditional energy analysis focusing on terminal energy consumption could lose effectiveness on urban scale and new approach needs the combination of end technical energy saving with source reduction of product consumption.