Provided is a method of correcting an ionosphere error, a system of a precise orbit determination using the same and a method thereof. The method includes the steps of: a) determining a time of a highest elevation angle of a GPS satellite per one pass of each GPS satellite received at a LEO satellite or a receiver on a ground; b) determining a minimum total electron content found from an ionosphere model of the determined time per one pass of each GPS satellite; c) determining a total electron content directly calculated from the LEO satellite or a single frequency GPS data; d) determining an ionosphere error value of a single frequency GPS data by combining the minimum total electron content and the directly calculated total electron content; and e) correcting pseudorange data or carrier phase data based on the determined ionosphere error value.