Disclosed is directed to a navigation system using POI code numbers, and an operating system and method thereof. In the system according to the invention, information matching to real states, including POI code numbers, local information, and business information, is stacked on a database to provide a user with geographic information obtained from searching an identical one matching to a POI code number entered by the user. If there has been an update for the geographic information, new POI code numbers are endowed with the updated information and then stored with being associated to the endowed POI code number. The invention also abstracts pre-registered user information using a vehicle navigation system and then updates the geographic information by transferring the POI code number and the undated information thereof to the vehicle navigation system through a communication network in accordance with the abstracted user information. The invention is able to simply search a destination by means of the POI code number.