Structural damage often happens in rotating machinery such as steam engines, aircraft engines, and compressors due to the high-speed rotating of the shaft. The most common structural damages in rotating machinery are rotor shaft crack, rotor to stator rub, and bolts looseness and so on. In the present paper, the model based identification method is used to detect single structural damage such as crack, rotor to stator rub, pedestal looseness, and also, coupling fault such as rotor to stator rub and crack, crack and pedestal looseness. Utilizing the characteristic that equivalent loads of rub forces are internal forces, and the equivalent loads of the crack are external moments, the coupling faults of crack and rub-impact and crack and pedestal looseness are analyzed and exampled. The merit of the method is that it is an online diagnosis method, which provides early warning of machine failure. Theoretical simulation and laboratory testing are conducted to validate the method.