In this paper, a method for inversion of sound velocity profile in multibeam survey is pre-sented. Firstly, the sound velocity profile samples are analyzed with empirical orthogonal function (EOF) and the reconstruction coefficients are calculated by sound velocity perturbation matrix and previous order of EOF. Secondly, the reconstruction coefficients of EOF are estimated by simulated annealing algorithm, the target function is constructed with the seafloor distortion which is obtained by multibeam sounding. Finally, the inversion of sound velocity profile is reconstructed. The analysis of examples show that the inversion of sound velocity profile is closer to the real sound velocity profile and the seafloor corrected with inversion of sound velocity profile is closer to the real seafloor.