Few insights have been gained on how the complexity of supply chains affects energy footprint of an urban economy. To fill in this research gap, we develop a new approach to systemically assess the impact of changing structure of supply chains on urban energy footprint over time. With the integration of input-output analysis, structural decomposition analysis and ecological network analysis, the approach is capable of identifying and quantifying the drivers that control urban energy flows associated with simple and complex supply chains. Using the city of Beijing as demonstration, we find the contribution of complex supply chains to the total energy footprint controlled by urban demand increased drastically from 12% in 1985 to 47% in 2012. Supply chain complexity has become a stronger driver over 2000-2012 than control structure and population in altering the city's energy footprint. The lowering of network efficiency due to the increased complexity of supply chains may destabilize urban energy systems and should be treated with caution in managing energy flows of cities. This approach can be generalized to assess how the dynamics of energy and environmental footprints is affected by evolving supply chains in economy. (C) 2019 Elsevier Ltd. All rights reserved.