The invention provides a three-dimensional animation video navigation method and a system thereof. The method comprises the following steps: determining the position of a user; judging whether the user enters the display scope of three-dimensional animation video data; selecting the three-dimensional animation video data by using a data enquiry module; calculating the position of a three-dimensional animation video display frame by using a three-dimensional animation video display module and playing on a display device; and judging that the position of the user is away from the display scope of the three-dimensional animation video data by using a position judging module to finish displaying a three-dimensional animation video. The navigation system comprises a position positioning module, the position judging module, a three-dimensional animation video data base, the data enquiry module and the three-dimensional animation video display module. The three-dimensional animation video navigation method and the system thereof are used for displaying a three-dimensional scene close to reality, help the user to quickly determine the current position before the change of a road and select an accurate path. Meanwhile, the invention also can achieve the functions of tourism navigation, shopping navigation, parking navigation and the like.