Cities (“urban superorganisms”) exhibit metabolic processes. Disturbance of these processes results from the high throughput of the socioeconomic system as a result of the flow of resources between it and its surroundings. Based on systematic ecology and emergy synthesis, we developed an emergy-based indicator system for evaluating urban metabolic factors (flux, structures, intensity, efficiency, and density), and evaluated the status of Beijing's environment and economic development by diagramming, accounting for, and analyzing the material, energy, and monetary flows within Beijing's metabolic system using biophysically based ecological accounting. We also compared the results with those of four other Chinese cities (Shanghai, Guangzhou, Ningbo, and Baotou) and China as a whole to assess Beijing's development status. From 1990 to 2004, Beijing's metabolic flux, metabolic intensity, and metabolic density increased significantly. The city's metabolic processes depend excessively on nonrenewable resources, but the pressure on resources from outside of the city decreased continuously. The metabolic efficiency increased by around 12% annually throughout the study period. Beijing had a highest metabolic fluxes and density compared with the four other cities; its metabolic efficiency was lower, and its metabolic intensity was higher. Evaluating these metabolic indicators revealed weaknesses in the urban metabolic system, thereby helping planners to identify measures capable of sustaining these urban metabolic processes.