As an alternative method, an algorithm for bathymetry inversion using vertical deflections is proposed. Firstly, the formulas for the bathymetry inversion from north and east components of vertical deflections are derived and the data processing is introduced. Then a local area in the South China Sea is selected as an example to experiment the method. The bathymetry inversion based on gravity anomaly was also conducted for a comparison. The results show that the bathymetry derived from the north component of the vertical deflections have almost the same accuracy as that derived from gravity anomalies and the results derived from the east component have the poorest accuracy. The experiment’s results also show that accuracy of the derived bathymetry can be improved if the fitting parameters are adjusted according to the water depths. In summary, among the gravity field products used in this study, although the gravity anomaly yielded the best performance in the bathymetry inversion, the vertical defections can still be used as supplements, especially in areas where accurate vertical deflections exist. This is because deriving gravity anomaly from altimetry observations needs additional data and calculation efforts.