AbstractCities are increasingly linked to domestic and foreign markets during rapid globalization of trade. While transboundary carbon footprints of cities have been recently highlighted, we still have limited understanding of how carbon emission linkages between sectors are reshaping urban carbon footprints through time. In this study, we propose an integrated input‐output approach to trace the dynamics of various types of carbon emission linkages associated with a city. This approach quantifies full linkages in the urban carbon system from both production‐ and consumption‐based perspectives. We assess the dynamic roles that economic sectors and activities play in manipulating multiscale linkages induced by local, domestic, and international inputs. Using Beijing as a case study, we find that imports from domestic and foreign markets have an increasing impact on the city's carbon footprint with more distant linkages during the period from 1990 to 2012. The manufacturing‐related carbon emission linkages have been increasingly transferred outside the urban boundary since 2005, while the linkages from the energy sector to services sectors remain important in Beijing's local economy. Applying systems thinking to input‐output linkage analysis provides important details on when and how carbon emission linkages evolved in cities, whereby sector‐oriented and activity‐oriented carbon mitigation policies can be formulated.