Aiming at the problem that the orthogonal frequency division multiplexing (OFDM) underwater acoustic communication is sensitive to Doppler frequency shift, a Doppler estimation and compensation algorithm for OFDM underwater acoustic communication based on non-uniform fast Fourier transform ( NUFFT) is proposed. The type-2 NUFFT technique is introduced into the OFDM underwater acoustic communication and utilized to perform Doppler factor grid compensation on the received signal. And the estimation of underwater acoustic channel is obtained through the sparse Bayesian learning. Then the minimum sparse energy of the underwater acoustic channel is used as the Doppler factor judgment criterion to obtain a high-precision Doppler estimation. Simulation results show that when the signal to noise ratio (SNR) is greater than 5 dB, the root mean squared error (RMSE) of the proposed method is better than 1×10 -5 . And the bit error rate (BER) of the system decreases with the decrease of the RMSE of Doppler estimation. The results of the sea trial show that the relative radial velocity between the two ships obtained with the proposed Doppler estimation method is consistent with the actual situation. And the average BER after decoding is better than 8. 33 × 10 -4 . Simulation and sea trial results demonstrate that the proposed algorithm can effectively estimate Doppler factor and reduce the system bit error rate.