The multi-beam bathymetry system can obtain fine and comprehensive data on underwater topography. Nevertheless，such data are complicated and time-consuming to process，and the differences in data quality caused by different processing levels cannot be ignored，which necessitates the use of the filtering tools in the software to assist with multibeam data processing. To address the problems of complicated and difficult filtering theory and different filtering methods and effects，this paper analyzes the effect of filtering tools in dredging surveys by combining the commonly used filtering tools in the QINSY software and the Yidiantong software with engineering practice. Furthermore，the paper determines the filter selection for corresponding dredging projects. In this way，the paper shortens the multi-beam data processing cycle and reduces the probability of large differences caused by manual data processing.