To solve the deformed seabed topography caused by the representative error sound velocity profile (SVP) in the flat seafloor during measuring the depth of sea by multibeam systems, a sound velocity profile inversed and seafloor topography corrected method is proposed on the basis of the seabed observation. Looking on the incidence angles and the travel time of beam as the input parameters, the function relationships are built up between the beam displacement and the travel time of the error sound velocity. Then, the modified SVP, which was approximated to the true SVP, is inversed by the indirect adjustment and the Levenberg-Marquardt (LM)method. Thus, correcting the distorted terrain is achieved. Through the field data validating, results show that the inversed SVP is more converged to the original SVP than that of the error SVP. Meanwhile, the distorted terrain caused by the sound velocity errors can be reduced effectively by the proposed inversion method, and the STD (standard deviation) of the modified depth is reduced by 50% above.