This paper presents a novel approach for incomplete text system. Which is based on hypergraph model clustering by using the set-pair analysis, and in which the similar, different and anti-contact connectivity of Set-pair and the similarity value of set-pair are used. After hypergraph model set up, a hypergraph partitioning algorithm is used to find clusters. This new method can eliminate disadvantageous factors and decrease the number of dimensions of the incomplete text data and enhance the speed largely and precision of text clustering. The experimental results show that the algorithm is feasibile and efficient.