The paper focuses on the application of structural analysis based on mathematical model of air supply system of fuel cell to realize the objective of fault detection and isolation. The model of the air supply system which is based on volumetric air compressor is transformed into structural state equations in order to simplify the procedure of structural analysis. A state of art mentioned air compression system is given. A faults tree is provided before the application of the FDI approach. The paper is concerned on how to generate analytical redundancy relations in dynamic states. The results show that all faults in specifications can be detected but not isolated.