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An integrated scenario analysis methodology has been proposed for zero-carbon energy system in perspectives of social-economy, environment and technology. By using the methodology, service demands in all sectors were estimated based on social-economic data, and then the best technology and energy mixes were obtained to meet the service demands. The methodology was applied to Japan toward zero-carbon energy system out to the year of 2100, and three different scenarios of nuclear power development are considered in light of the Fukushima accident: (i) no further introduction of nuclear, (ii) fixed portion and (iii) no limit of nuclear. The results show that, zero-carbon energy scenario can be attained in the year 2100 when electricity will supply 75% of total energy consumption, and three power generation scenarios were proposed, 30% renewable and 70% gas-carbon capture and storage (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, Scenario 2 is rated as the most balanced scenario by putting emphasis on the availability of diversified power source, considering the inter-comparison of the three scenarios from the four aspects of cost, CO<inf>2</inf> emission, risk and diversity.