The embodiment of the invention discloses a method and system for carrying out debugging on a base station database based on GPS positioning. The method comprises the steps that one cell in a mobile communication network serves as a current cell, LBS positioning is continuously and repeatedly carried out on all mobile phone terminals j not moving in n mobile phone terminals in a current cell coverage area m times, and m LBS positioning position coordinates of the n mobile phone terminals are obtained, and the average value of the m LBS positioning position coordinates is obtained; the average value of the LBS positioning position coordinates, obtained m times, of the mobile phone terminal j and the positioning position deviation distances between GPS positioning position coordinates are obtained; the average value of the positioning position deviation distances of the n mobile phone terminals is obtained, and whether the base station information of the current cell in the base station database is accurate or not is determined according to the fact about whether the average value is larger than the preset threshold value. According to the method and system, automatic inquiry of the mistaken base station information in the base station database can be achieved.