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The condition of rotor system must be assessed in order to develop condition-based maintenance for rotating machinery. It is determined by multiple variables such as unbalance degree, misalignment degree, the amount of bending deformation of the shaft, occurrence of shaft crack of rotor system and so on. The estimation of the degrees of unbalance and misalignment in flexible coupling-rotor system is discussed. The model-based approach is employed to solve this problem. The models of the equivalent extal loads for unbalance and misalignment are derived and analyzed. Then, the degrees of unbalance and misalignment are estimated by analyzing the components of the equivalent extal loads of which the frequencies are equal to the 1 and 2 times running frequency respectively. The equivalent extal loads are calculated according to the dynamic equation of the original rotor system and the differences between the dynamical responses in normal case and the vibrations when the degree of unbalance or misalignment or both changes. The denoise method based on bandpass filter is used to decrease the effect of noise on the estimation accuracy. The numerical examples are given to show that the proposed approach can estimate the degrees of unbalance and misalignment of the flexible coupling-rotor system accurately.