An integrated scenario analysis methodology has been proposed for zero-carbon energy system in perspectives of social-economy, environment and technology. In the methodology, firstly various service demands were estimated based on social-economic data, and best technology and energy mixes were obtained using the optimization model to meet the service demand. The methodology has been applied to Japan toward zero-carbon energy system out to 2100. The results show that, in the end user side, zero-carbon energy scenario was obtained based on 75% on electricity and three power generation scenarios were proposed, 30% renewable and 70% gas-CCS in scenario 1, respective one third nuclear, renewable and gas-CCS in scenario 2, and 60% nuclear power, 20% renewable and 10% gas-CCS in scenario 3. Finally, the scenario 2 with balanced diversity in nuclear, renewable and gas-CCS was recommended based on comprehensive inter-comparisons. The feasibility of the proposed methodology has been demonstrated. (C) 2014 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/3.0/).