Water depth measurement requires the establishment of one or more tidal stations in the survey area for synchronous water level observation, and finally the water depth is estimated to the depth datum. The non-tidal observation measuring has high efficiency and avoids the water level correction error caused by tidal observation in traditional sounding. Therefore, non-tidal observation measuring has become an effective water depth measurement method in offshore and inland water. However, datum conversion in non-tide operation is mostly based on the polynomial fitting method. The accuracy of this method is influenced by the distribution of datum control points, topographic relief and operation ranges. In this paper, we present a method to construct a depth datum geodesic height model, which can directly obtain a bathymetric database of depth data in a GNSS bathymetric survey. The model incorporates the continuous depth datum and the mean sea level of geodetic height in the same area. Through the numerical simulation of tidal wave motion in regional water, the tidal model is obtained. Based on the grid model, the tidal level is extracted from the tidal model for harmonic analysis, and a continuous depth datum model is established. Mean sea level geodetic height is from the CNES-CLS2015 Average Sea Surface Model. In this paper, the model is confirmed in the South Yellow Sea area. The results show that the accuracy of the depth datum model, and the depth datum geodetic height model meets the accuracy requirements of the datum.