On the basis of density functional theory and electronegativity equalization princi-ple, a new scheme has been developed for determination of atomic charges and bond charges in large molecules. In the new scheme, the molecular electron density ρmol(r) is partitioned as where ρα(r) and ρα-β(r) are the electron densities located on the atom α and bond α-β, respectively. The parameters A, B, C and D are the valence-state electronegativity and valence-state hardness. They are obtained by calibrating through model molecule calculations and are transferable and consistently usable for calculating the charge distributions in large molecules. The new scheme is tested through determination of atomic charges and bond charges in several large molecules. It has been shown that the re-sults of atomic charges and bond charges obtained by the new scheme dovetail those obtained by ab initio method very well. In addition, the new scheme presented here has the advantage of simplicity, rapidness and easy perform as well, so that it provides an efficient and practi-cal method for calculation of the charge distribution for a macromolecular system.