Abstract: The existing methods of Doppler estimation in UnderWater Acoustic (UWA) communication generally assume that the Doppler factor of each path is equal in multipath channel. But when the Doppler factors are different from each other, such methods can not estimate the Doppler factor correctly, resulting in significant compensation error. By analyzing the sparsity of the UWA channel, a novel method of non-uniform Doppler estimation is proposed, which is based on the sparse representation theory. By using the over-complete dictionary combining UWA multipath channel and non-uniform Doppler sparsity, the method transforms Doppler estimation of each path into sparse solution reconstruction, achieving accurate estimation of non-uniform Doppler factor. Simulation results show that the proposed method can estimate not only the quite different Doppler factors but also the large Doppler frequency offset. Therefore, it is especially important for Doppler estimation in high-speed mobile UWA communication.