We developed a modified localization scheme for the three-dimensional elongation method for calculations on large molecular systems. The scheme is based on the individual small dimensional elongation units, and its high efficiency is verified by test calculations on a protein molecule by using the HF/STO-3G basis set. The results show that the modified scheme performs localization about two times faster than the original scheme with the same accuracy. The acceleration increases with the system size. Therefore, the modification to the localization scheme makes the elongation method more efficient for three-dimensional large molecular calculations. (C) 2013 Elsevier B. V. All rights reserved.