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Specific emitter identification (SEI) identifies targets mainly by unintentional modulation of the signal. However, due to the high energy of the primary signal, once the primary signal changes, the recognition becomes less effective or even impossible using a feature database that is not updated. In this paper, we propose to use a mutual information improved variable mode decomposition (VMD) algorithm to suppress the primary signal phase of the transmitter. Furthermore, we simulate the feature extraction of the unintentional phase modulation of the transmitter signal and use support vector machine (SVM) for individual identification. The simulation results show that the algorithm improves the recognition rate by about 6% (0 dB) compared to the retained primary signal. The results demonstrate that our proposed phase suppression technique improves the adaptability and accuracy of individual identification of transmitters.