Semiotic analysis is often used for describing the inter-relationship of structure, function and behavior of any artifacts as the means for designing various computerized tools for machine diagnosis and operation procedure. In this study, a graphical method called Multilevel Flow Models (MFM) is applied for supporting machine maintenance work of commercially available Micro Gas Turbine System (MGTS), to describe and handle the relationships between goals and functions that exist in various parameters of MGTS including signal, alarm and fault. A new three-step method including alarm validation, fault condition checkup and fault identification is proposed for fault diagnosis based on MFM. A trial software has been developed by using Visual C++ and Excel for monitoring and diagnosing the MGTS based on the proposed fault diagnosis method. And it was tested by several typical actual fault cases, to show that the proposed method is efficient to monitor the running state of MGTS and to diagnose the real reason of faulty message from the operation software provided by the vendor of Micro Gas Turbine.