Abstract: The direction of arrival (DOA) estimate by bathymetric side-scan sonar is affected by the amplitude-phase errors of array elements and low signal to noise ratio (SNR). For this problem, a modified beam space weighted subspace fitting (MBS-WSF) algorithm is proposed. Firstly, the total least squares-estimation of signal parameters via rotational invariance techniques (TLS-ESPRIT) algorithm is used to pre-estimate the echo direction; secondly, the uniform linear array (ULA) is divided into multiple subarrays, and weighted beamforming is performed for each subarray in the pre-estimated direction; thirdly, the WSF algorithm is used to construct cost function; and finally, the high precision DOA estimation result is obtained by using the damped Newton method. The simulation results show that, the proposed algorithm improves the mean square error of angle estimation by about 0.03° compared with the WSF algorithm in the presence of amplitude-phase errors in array elements. The analysis of sea trial data shows that the mean square error of the proposed algorithm is better than that of WSF algorithm, and its relative bathymetric accuracy is improved by about 9.8 percentages, which shows that the proposed algorithm is superior to the WSF algorithm, and can achieve high precision DOA estimation under the conditions of the array elements with amplitudephase errors and low signal to noise ratio.