The Doppler effect critically degrades the performance of orthogonal frequency division multiplexing (OFDM) systems in general. This problem is significantly worse for underwater acoustic (UWA) communication systems due to the distinct characteristics of the underwater channel, resulting in the loss of orthogonality among sub-carriers. In order to compensate Doppler shifts, including phase noise and multipath channels in realistic communication scenarios, the joint of channel estimation and ICI reduction is often performed. However, the accuracy depends on the channel estimation and the FFT size, while this leads to increased computational complexity at the receiver. To achieve this dual goal in the actual underwater communication environment, a novel pilot structure in the frequency domain has been applied to overcome the channel impulse response (CIR) variation in a block period. The coarse Doppler shift is firstly estimated by using the received pilot signal. Afterward, the study takes advantage of the flexibility provided by non-uniform fast Fourier transform (NFFT) in choosing the sampling points to construct a fast and stable Doppler frequency Compensation Matrix-based NFFT (DCMN) to fine compensate the Doppler phase shift. Finally, this study shows the improvement of the proposed method’s performance by actual experimental measurements and simulations.