In some multi-beam bathymetric sonar applications, accuracy of the DOA estimation algorithms presently used reduces for the seafloor backscattering signals dissatisfying the point sources assumption, while the DOA estimation algorithms based on assumption of distributed source model have a potential to solve it well. However, most existing distributed source algorithms fail to distinguish incoherent sources apart. Although Toeplitz method has been proposed and tested effective to the problem, it has low estimation accuracy and can’t estimate the parameters of angle expansion. Aiming at the DOA estimation problem of multi-beam bathymetric sonar, a generalized MUSIC algorithm based on spatial smoothing is proposed and proved to be effective by formula derivation. Its accuracy and performances under different SNR are given via computer simulation. Finally, the method is tested with experimental data of multi-beam bathymetric sonar.