Cities play a crucial role in the implementation of carbon emission mitigation policies since most CO2 emissions are related to energy consumption in urban areas. Recent years, environmentally extended multi-regional inputoutput tables (EEMRIO) are emerged to reveal regional environment impact considering upstream supply chains crossing regional boundaries. However, city-scale MRIO has not been fully addressed since more focus has been located on national or prefectural level evaluation. For quantifying city-scale emission considering regional energy flow, we apply the input-output table of Tokyo to evaluate energy consumption at the city scale, and the results provides one of the the most detailed sector classification from a wide range of city emission studies. In Japan, Tokyo is considered to be representative of the contemporary Japanese urban energy structure, and its energy consumption and associated CO2 emissions are of major importance when making city-scale carbon mitigation policies. Here, domestic production for Tokyo and other regions is used to quantify the direct and indirect emissions arising from Tokyo final consumption. Our results are divided into sector-specific and fossil fuel source-specific (coal, crude oil, and natural gas) for both direct and indirect emissions. The major findings are as follows: (1) The transportation sector accounts for the largest share of direct emissions in Tokyo. (2) The energy supply, construction, private service sectors account for the largest share of indirect emissions in Tokyo. (3) There are three scopes of emission responsibility evaluated in this study: direct emission before allocation (BE) as 12.88 MtC, after allocation (AE) as 18.91 MtC, and the total including indirect emissions is 27.24 MtC, which is more than twice the direct emissions before allocation. The detailed and energy consumption and emission inventory may be essential for emission responsibility allocation to overcome geographical boundary, therefore, contributes to varied scales of carbon reduction policies.