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Weighted fuzzy clustering algorithm is proposed and applied in management zones of soil nutrients. In the algorithm, the determination of the weight of different soil nutrients is a key step. Two methods are used to determine the weight. One is the principal component analysis (PCA). The other is coefficient of variation (C.V).To verify above methods, soil nutrients of N, P, K were sampled at the experimental site, a field in Yushu City of Jilin Province, and then the weighted fuzzy clustering algorithm was used and the number of the management zones was determined. The effectiveness of the weighted fuzzy clustering method was validated by comparing with the traditional fuzzy clustering method. The results show that the weighted fuzzy clustering method is more reasonable and more practical and can be used to support precision fertilization.