Disclosed is a method for preparing a polyester resin, wherein phosphate additives are used in preparing polyester resin to improve the reactive property of the esterification reaction or transesterification, as well as the flame retardancy property and the color stability of a polyester resin. The method for preparing a polyester resin comprises the steps of: carrying out an esterification reaction and/or an ester exchange reaction of a diacid component and a diol component in a presence of phosphoric acid derivatives, wherein the diol component comprises a primary diol and isosorbide, and wherein a reaction time of the esterification reaction or the ester exchange reaction is reduced and the remaining rate of isosorbide in the main chain of the polyester resin is increased.