Disclosed is a navigation system and displaying method thereof, which controls the level of protrusion for each piece of indication data displayed on a 3-D screen of the navigation system based on its criticality so as to maximize the legibility of the driver. More specifically, the navigation system includes a GPS receiving member which receives GPS location information, a map data storage member which stores map data including a plurality of indication data, a controlling member which requests a display scope of the map data, corresponding to the received GPS location information, and at least one set of indication data within the display scope, and 3-D data-processes said indication data so that it can be displayed so that the most important data is protruding the most to the driver, and a display member which displays the map data containing the 3-D data-processed indication data.