Abstract: In the traditional mode for underwater measurement, the vessel generates unavoidably pitch, roll and heave by the water flow, wind, waves and other effects. These effects produce great error of bathymetric survey, but the error is difficult to eliminate because of the randomness of wave. The effect of heave can be eliminated by attitude instrument, but the equipment is not widely used in the coastal and inland river basins because of the high cost of the equipment. No tide sounding system can weaken the heave of transducer, but this method requires the normal height of every control points by leveling and the tide data. This paper analyzes the correction method and principle of the heave, and researches the signal of GPS-RTK height and how to extract the heave, and proposes the heave correction of transducer using GPS-RTK height which can weaken the heave, improve the accuracy in the bathymetric survey with tide.