Sound velocity errors often lead to distortion of seafloor topography in multibeam bathymetric data processing. The current method of sound velocity profile (SVP) inversion has the problems of small application scope of the inversed equivalent SVP (ESVP) and terrain distortion calculated by inversed SVP under the condition of water depth consistency constraint in overlapping line area. In this article, we propose a method of SVP inversion using the empirical orthogonal function (EOF) and differential evolution (DE) algorithm. First, EOF is used to decompose the SVP matrix. Then, the water depth discrepancy between the check line and the main survey line is used as the objective function instead of the discrepancy of overlapping line area, and DE is used to find the optimal time coefficient. Finally, the SVP is reconstructed to correct the seabed topography. The method was verified by experiments in shallow and mid-deep water, and the mean absolute and standard deviation of the corrected bathymetric discrepancy values are about 50% of those before correction.