A positioning navigation system using identification tags and a method thereof is provided. The system and method are applied to an area having a plurality of identification tags to position and navigate a mobile apparatus. The system includes a plurality of identification tags and a mobile apparatus. The method includes steps of accessing unique position data stored in at least one identification tag and generating position information of the mobile apparatus according to the unique position data stored in the at least one identification tag and a geographic data of the area. The unique position data of each identification tag corresponds to a coordinate position of the geographic data of each identification tag within the area.