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Inverse synthetic aperture radar (ISAR) imaging of ship targets is very important in the national defense. For the high maneuverability of ship targets, the Doppler frequency shift of the received signal is time-varying, which will degrade the ISAR image quality for the traditional range-Doppler (RD) algorithm. In this paper, the received signal in a range bin is characterized as the multi-component polynomial phase signal (PPS) after the motion compensation, and a new approach of time-frequency representation, generalized polynomial Wigner-Ville distribution (GPWVD), is proposed for the azimuth focusing. The GPWVD is based on the exponential matched-phase (EMP) principle. Compared with the conventional polynomial Wigner-Ville distribution (PWVD), the EMP principle transfers the non-integer lag coefficients of the PWVD to the position of the exponential of the signal, and the interpolation can be avoided completely. For the GPWVD, the cross-terms between multi-component signals can be reduced by decomposing the GPWVD into the convolution of Wigner-Ville distribution (WVD) and the spectrum of phase adjust functions. The GPWVD is used in the ISAR imaging of ship targets, and the high quality instantaneous ISAR images can be obtained. Simulation results and measurement data demonstrate the effectiveness of the proposed new method.