With the improvement of marine vibration index, the current static shafting alignment method is not yet suitable. The effect of shafting misalignment on rotating system vibration is not clear. Based on the mechanics analysis on elastic coupling of three different types of misalignment, the dynamic models of misalignment excitation are first established, and this dynamic model is also verified by bench test. The results show that under the excitation of shaft misalignment, the relative errors between the simulation results for the situations of synchronous harmonic, second harmonic and peakpeak vibration and the bench test data are less than 20%. Moreover, it is found that the increasing misalignment of elastic coupling results in strong vibration, accompanying with increasing excitation amplitude.