A data updating system includes a navigation device running according to a predefined application program; and a server providing the navigation device with a differential data file for updating a database containing road network data. The navigation device includes a navigation memory storing a local database in an updating data format in which the road network data is arranged in the order of data types and to be updated with the differential data file; and a navigation controller that converts data stored in the local database so as to have the reference data format in which the road network data is arranged in the order of connection of the road network to be referenced to by the application program. The server includes a server controller that outputs the differential data file to be provided to the navigation device.