This paper presents a multi-criteria evaluation methodology for nuclear fuel cycle options in the term of sustainability. Starting from the general sustainability concept and the public acceptance questionnaire, a set of indicators is defined reflecting specific criteria for the nuclear fuel cycle options evaluation. 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, 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 system are examined by using the proposed methodology. The assessment process and result can give us some guidance in the nuclear fuel cycle evaluation even under the constraint of limited data.