When there appears the relative motion between the sound source and the receiver, the received tonal signal will produce Doppler shift, and the Doppler information is relevant to the motion parameters of the target. According to the acoustic Doppler shift frequency, we propose the Doppler-warping transformation. The phase linearization of the Doppler signal can be realized by using the transformation. Then, we deduce the warping operator and propose an algorithm for estimating the target motion parameters by using the proposed transformation. Firstly, the Doppler-warping operator under different motion parameters is constructed. Secondly, the time resampling of the received time-domain signal is performed by using the operator. Then, the spectral function of the transformed signal is calculated. Finally, the spectral function entropy is minimized to estimate the objective parameter. The simulation results show the effectiveness of the proposed method. For a low signal-to-noise ratio of sea trial data, where the real speed of a fishing boat is 4.5 m/s, the result from the traditional minimum mean square error (MMSE) velocity estimation method is 5.2 m/s, and the estimation error is 15.56%. The proposed Doppler-warping transform method can estimate the target velocity more accurately, specifically, it is 4.7 m/s and its corresponding estimation error is 4.44%.