Reducing environmental impacts related to resource use has been considered a significant challenge for sustainable development, but methodologies to assess national level impact decoupling have not been established adequately. For this, an economy-wide eco-efficiency analysis of Japanese material production and a decomposition analysis are conducted. Combining data from the Japanese life cycle inventory and input–output table, we calculate the eco-efficiency of 451 materials with respect to 13 impact categories and perform a decomposition analysis. Results indicate tendency that material groups, with larger share of value added and environmental impact to national total show lower eco-efficiency. Environmental impacts on foreign supply chains, especially in areas of resource consumption and global warming, are large. These findings imply the necessity of improving the processing of lower eco-efficiency materials, through, for example, intensifying decarbonization and circular economy, and strengthening the production of higher eco-efficiency materials to improve the eco-efficiency of Japan.