A method and apparatus for a navigation system detects a hidden point on a route on a monitor screen showing a three-dimensional map when visibility of the route begins to be lost, and provides a warning message including relevant information that is helpful to navigate the hidden point. The method includes steps of displaying a three-dimensional map image which includes an image of a route on which a user or user's vehicle is travelling, detecting a hidden point of the route on the three-dimensional map image at which the route becomes invisible by an obstruction object when viewed from a current position of the user, and notifying the user about the hidden point on the route thereby enabling the user to know the hidden point on the route in advance.