For fast Cholesky factorization, it is most important to reduce the number of nonzero elements by ordering methods. Generally, the minimum deficiency ordering produces less nonzero elements, but it is very slow. We propose an efficient implementation method. The minimum deficiency ordering requires much computations related to adjacent nodes. But, we reduce those computations by using indistinguishable nodes, the clique storage structures, and the explicit storage structures to compute deficiencies.