Complex energy and environment system, especially nuclear fuel cycle system recently raised socialconcerns about the issues of economic competitiveness, environmental effect and nuclear proliferation. Only underthe condition that those conflicting issues are gotten a consensus between stakeholders with different knowledgebackground, can nuclear power industry be continuingly developed. In this paper, a new analysis platform has beendeveloped to help stakeholders to recognize and analyze various socio-technical issues in the nuclear fuel cycle systembased on the functional modeling method named Multilevel Flow Models (MFM) according to the cognition theoryof human being. Its character is that MFM models define a set of mass, energy and information flow structures onmultiple levels of abstraction to describe the functional structure of a process system and its graphical symbol representationand the means-end and part-whole hierarchical flow structure to make the represented process easy to beunderstood. Based upon this methodology, a micro-process and a macro-process of nuclear fuel cycle system wereselected to be simulated and some analysis processes such as economics analysis, environmental analysis and energybalance analysis related to those flows were also integrated to help stakeholders to understand the process of decision-making with the introduction of some new functions for the improved Multilevel Flow Models Studio, and finallythe simple simulation such as spent fuel management process simulation and money flow of nuclear fuel cycleand its levelised cost analysis will be represented as feasible examples. Complex energy and environment system, especially nuclear fuel cycle system recently raised socialconcerns about the issues of economic competitiveness, environmental effect and nuclear proliferation. Only underthe conditions that those conflicting issues are gotten a consensus between stakeholders with different knowledgebackground, can nuclear power industry be continuingly developed. In this paper, a new analysis platform has been built to help stakeholders to recognize and analyze various socio-technical issues in the nuclear fuel cycle systembased on the functional modeling method named Multilevel Flow Models (MFM) according to the cognition theory of human being. Its character is that MFM models define a set of mass, energy and information flow structures on multiple levels of abstraction to describe the functional structure of a process system and its graphical symbol representation and the means-end and part-whole hierarchical flow structure to make an represented process easy to beunderstood. Based upon this methodology, a micro-process and a macro-process of nuclear fuel cycle system were selected to be simulated and some analysis processes such as economics analysis, environmental analysis and energybalance analysis related to those flows also integrated to help stakeholders to understand the process of decision-making with the introduction of some new functions for the improved Multilevel Flow Models Studio, and finally the simple simulation such as spent fuel management process simulation and money flow of nuclear fuel cycle and its levelized cost analysis will be represented as feasible examples.