Based on density functional theory, a general arom-bond electronegativity equalization method (general ABEEM), which explicitly considers the structure of the double bond for the first time, is developed for prediction of charge distributions in polypeptides. Parameters employed in this model are determined and discussed. By testing, it is used to calculate the charge distributions of the polypeptides C32N9O6H49 and C23N4O3H26 as examples, and the results show good agreement with those obtained by the accurate ab initio method, which implies that the general ABEEM method is reasonable and applicable.