Abstract Indonesia’s archipelagic territory provides constraints for determining a seamless vertical datum throughout the region. The main constraint is how to connect the vertical datum between islands separated by sea. To define the physical height system of land areas, it usually refers to the Mean Sea Level (MSL), which has different values in each area, and the ideal MSL information is not yet available throughout regions with a minimum data duration of one cycle of 18.6 years. To overcome this constraint, in this research, another alternative method is used: applying a vertical datum that refers to a physical geoid reference surface, namely Mean Dynamic Topography (MDT) using Altimetry satellite data. The study area is Java Island and its surroundings, using vertical information from Geodetic Control Point stations, which also function as Tidal stations in the Indonesian Geospatial Reference System network. The range of MDT deviation values obtained from the Satellite Altimetry with Geodetic Ground Control data is ± 2 meters, which is a good value for coastal areas facing the open sea. This shows that the application of the geoid and MDT models can be used as an alternative, seamless MSL approach in the Java Island region and its surroundings.