Abstract: Systematic residue is a common problem in strip splicing of the multi-beam sounding system. We proposed in this paper a method to weaken the influence of the systematic residual error based on the topographic spectrum analysis. A comparison is also made with the traditional method. Different with the traditional method, this method does not require continuous matching of adjacent strip ping, and thus we may avoid inconsistent problem of terrain long wave caused by ping mismatching. In addition, polyhedral function can be obtained by measuring the wave band overlap region, and signal can also be fitted signal non overlap ping regions. The evaluation indexes of the optimal parameters can effectively evaluate the short wave term and the long wave term signal. And the multifaceted function can not only obtain the overlap ping region long wave term signals of the measured strip, but also the fitting signal of the non-overlap ping region. The experimental results show that the impact of the residual error of the sounding data processed by the topographic spectrum analysis method has been greatly improved.