Complex energy and environment system, especially nuclear fuel cycle system recently raised social concerns about the issues of economic competitiveness, environmental effect and nuclear proliferation. Only under the condition that those conflicting issues are gotten a consensus between stakeholders with different knowledge background, can nuclear power industry be continuingly developed. In this paper, a new analysis platform has been developed to help stakeholders to recognize and analyze various socio-technical issues in the nuclear fuel cycle system based 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 the represented process easy to be understood. 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 energy balance 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 finally the simple simulation such as spent fuel management process simulation and money flow of nuclear fuel cycle and its levelised cost analysis will be represented as feasible examples.