The indirect greenhouses gas emission (GHG) embodied in the key urban materials purchased outside the city boundary (Scope 3) are often ignored in traditional city GHG studies, mostly concentrating on the emissions occurring inside the city (Scope 1) and emissions by the purchased electricity out of boundary (Scope 2). And there is little research on the structural analysis of the upstream supply chain for Scope 3. However, a comprehensive urban GHG accounting system is the basis for cities to make appropriate mitigation measures. Identifying the main embodied GHG that dominate the emissions in upstream supply chains can help focus attention on the largest emitters and offer insights into where climate mitigation efforts should be directed. Thus, in this study the Economic Input Output – Life Cycle Assessment (EIO-LCA) approach was used to evaluate the embodied GHG emissions from Scope 3 and to explore the related GHG emissions structure in the upstream supply chain based on the final demand for the key urban materials. And food, water, steel, cement, and fuel were selected as the representative urban materials based on the characteristic of Xiamen City. Our results demonstrate that the total embodied GHG emissions were 13,201.31 kt CO2e, very close to the direct GHG emissions from end-use sectors inside Xiamen city. Among the embodied GHG emissions, imported steel, fuels, cement, food, and water accounted for 56, 26, 13, 4, and 1% of the emissions, respectively. The main embodied GHG emissions contributors were found in the upstream supply chain and some related policy implications were presented. Compared to other cities, Xiamen had a relatively low per capita embodied GHG emission, which was 5.24 t CO2e lower than eight U.S. cities.