Unexpected events can have profound impacts on urban resource supply and consumption. The Great East Japan Earthquake (3.11 hereafter) triggered not only the planned blackout in the Tokyo Metropolitan Region soon after the disaster but also the energy shift to fossil fuels to recover from the disfunction of Fukushima nuclear power plants. Previous research has mainly focused on the direct energy consumption and carbon emissions of different sectors while the intensity and extensity of the impact on industries and the environment have never been empirically addressed. This study explores energy-use efficiency and carbon emissions in Tokyo from 2011 to 2015 through a lens of nexus using environmentally extended input-output analysis and community-wide carbon analytic approaches. Results show that the energy consumption is the largest exporter and importer of carbon emissions, whereas energy losses and carbon emissions caused by energy conversion and transmission are almost twice as much as those caused by the direct parts. Strong nexus effects among building and material, transportation, and energy consumption were observed. The 3.11 greatly impacted the energy structure and carbon emission patterns because of the increased consumption of coal for electricity. The share of energy consumption and carbon emissions by raw materials for construction also increased because of the increased demand for the reparation and reconstruction of buildings and transport systems. This structural change provided new scientific evidence for governments to implement decarbonization policies while preparing for unprecedented events.