An integrated and visual model EXCEM-MFM (EXergy, Cost, Energy and Mass - Multilevel Flow Model) has been proposed in this study to comprehensively analyze and evaluate the performances of thermal systems by coupling two models: EXCEM model and MFM. In the EXCEM-MFM model, MFM is used to provide analysis frameworks for exergy, cost, energy and mass four parameters, and EXCEM is used to calculate the flow values of these four parameters for MFM based on the provided framework. In this study, we used the tools and technologies of computer science and software engineering to materialize the model. Moreover, the feasibility and application potential of this proposed EXCEM-MFM model has been demonstrated by the example application of a comprehensive performance study of a typical High Temperature Gas Rector (HTGR) cogeneration system by taking into account the thermodynamic and economic perspectives.