The invention relates to a method for preparing modified polytrimethylene terephthalate. In esterification reaction, one or combination of more of straight-chain aliphatic dicarboxylic acid with the carbon number between 3 and 20, 1,4-cyclohexanedicarboxylic acid, straight-chain aliphatic diol with the carbon number between 4 and 20 and 1,4-cyclohexanedimethanol is taken as a third monomer; the use amount of the third monomer is 0.3 to 6.0 weight percent of the total weight of initial reaction raw materials; polyethylene glycol with the average molecular weight between 200 and 2,000, serving as a flexible chain segment, is added into the polymerization reaction, and the addition amount is 0.5 to 8.5 weight percent of the total weight of the initial reaction raw materials; and the modified polytrimethylene terephthalate is produced by the conventional polyester production process. The modified polyester chips prepared by the method have good spinnability and excellent crystallization capacity; in the spinning process, fibers are fully crystallized, so the stable crystallization rate is formed; when the fibers are heated and subjected to external stress, the crystallization rate of the stress parts of the fibers is stable, and the defect that PTT polyester fiber fabrics are susceptible to external force and high temperature loss can be effectively improved.