Matrix ordering is a key technique when applying Cholesky factorization method to solving sparse symmetric positive definite system Ax = b. Much effort has been devoted to the development of powerful heuristic ordering algorithms. This paper implements a sparse matrix ordering scheme based on hypergraph partitioning. The novel nested dissection ordering scheme achieve the vertex separator by hypergraph partitioning. Experimental results show that the novel scheme produces results that are substantially better than METIS.