The studies on regional differences are important basic works of regional development and ecological environment conservation. The application of Geographic Information System (GIS) in the study of regional difference of soil impoverishment is a main aspect of GIS in the soil geography. Taking Fujian Province as a case, the authors make the soil unit to be the regional unit, supported by GIS and multivariate statistical analysis methods, put forward a comprehensive index of reflecting the condition of soil impoverishment, calculate and output the grade maps of Fujian soil impoverishment. According to the shows of the map, the regional characters of soil impoverishment are analyzed. The conclusions are: (1) there are differences in area ratio of the soil nutrient in grade in Fujian Province, from small to middle to large, the area ratios in grade are 19.89%, 70.21% and 9.90%; (2) compared with two different land use types, the area ratio in grade of middle in forest land and dry land is higher than that in paddy field; (3) the regional distributions are the following: the grade of light impoverishment is mainly along the Daiyun mountains, middle mainly in the northwest and southeast Fujian Province, and large is mainly focused on several counties along the sea, such as Hui′an, Shishi, Yinjiang, Zhangpu, Yunxiao, Dongshan etc.. The study shows that the application of GIS in this field is advanced of application, efficient of the regional difference study and practical and credible of fruits.