Abstract: Variable rate fertilization is very important part of precision agriculture. Its core idea is based on that according nutrient content in soil to determine fertilizer amount, so as to achieve balance of soil nutrients. Now the conventional method for evaluating the soil nutrients is based on inspecting variations of each kind of soil nutrient separately, and this method can not comprehensive analysis. Therefore, the soil nutrients spatial difference after the variable rate fertilization was comprehensive evaluated by using a weighted fuzzy clustering algorithm. In 3rd field of 13th village in Gongpeng Town of YuShu city, comprehensive comparing of the soil nutrients of the field with no variable rate fertilization, with continuous variable fertilization for two years or five years was conducted. Result showed that the soil nutrients spatial difference was reduced obviously after continuous variable rate fertilization.