Global climate change has aroused widespread interest in reducing carbon emissions and increasing carbon sequestration. Thus, an urban carbon inventory must consider both emissions and sequestration. In this context, we analyzed the main contributors to the flows that comprise a city's carbon metabolic processes employing methods and concepts from ecological science. The carbon emissions and sequestration by urban carbon metabolic processes can be compared to ecological catabolism and anabolism, respectively. We used empirical coefficients to estimate the rates of carbon catabolism and anabolism and calculate the resulting carbon imbalance index. Our analysis reveals the contributions of individual metabolic actors and the distribution of the metabolic flows among them. Taking Beijing as case study, we found that the catabolic rate of the metabolic actors was more than five times the anabolic rate from 1995 to 2010, leading to a carbon imbalance index that was twice the average Chinese level. The major catabolic actors were the other services and domestic sectors. These catabolic rates were primarily influenced by the flows of electricity, heating energy consumption, and mobile energy consumption. The overall carbon imbalance resulted from greatly reduced metabolic flows in farmland anabolism due to conversion of farmland into urban land. Identifying the metabolic actors and flows in this manner will inform government mitigation efforts by identifying where reduction is required and guiding planning of appropriate mitigation actions. Our study also provides directions for conservation of the urban ecological environment.