To overcome the shortcomings of the traditional multibeam survey and data processing, a new method is presented for the precise determination of the instantaneous height at the multibeam transducer by the blend of GPS height and heave signals. Before signal blend, GPS height and heave signals need to be corrected first to the transducer center by attitude correction. Second, the GPS height needs to be checked and modified by heave check and modification itself. Butterworth and FFT (fast Fourier transformation) were used in the signal blend. Finally, FFT is thought to be appropriate in signal processing. The new method efficiently overcomes the shortcomings of the traditional method, and this is proven well by the MBS (multibeam bathymetric system) experiment.