The present invention relates in general to a navigation system, more particularly, to a navigation system and an operating method thereof, in which the navigation system shows the configuration of a complicated intersection a driver is about to enter, and displays where to turn and a progression rate of the car on the path the driver is headed to. The navigation system includes a map data memory for storing map data; an input unit including a route guiding module, in which a user inputs information and/or designates a travelling path, and the input unit provides information on a route from an entrance road of a car to an exit road from an intersection; a GPS receiver including a positioning module for detecting a present position of the car on the basis of position information provided from at least one GPS satellite; a Gyro sensor for detecting a rotation angle of the car; a controller, which uses the map data from the map data memory, route information from the input unit, information from the GPS receiver about the present position of the car, and route information from the Gyro sensor, to generate the configuration of an intersection the user is supposed to enter and an arrow indicating a driving route to the user, and to display a progression rate of the car along the route; and a display driving unit for displaying the configuration of the intersection and the arrow for route guidance, on the basis of output data from the controller, and for performing a graphic operation on the configuration, thereby a gradual progression rate of the car is indicated in the directional arrow.