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This paper presents a multi-criteria evaluation methodology for nuclear fuel cycle options in terms of energy sustainability. Starting from the general sustainability concept and the public acceptance questionnaire, a set of indicators reflecting specific criteria for the evaluation of nuclear fuel cycle options are defined.Particular attention is devoted to the resource utility efficiency, environmental effect, human health hazard and economic effect, which represent the different concerns of different stakeholders. This methodology also integrated a special mathematic processing approach, namely the Extentics Evaluation Method, which quantifies the human being subjective perception to provide the intuitionistic judgement and comparison for different options. The once-through option and reprocessing option of nuclear fuel cycle are examined by using the proposed methodology. The assessment process and result can give us some guidance in nuclear fuel cycle evaluation under the constraint of limited data.