The invention relates to a preparation method of polyethylene terephthalate-1,3-propanediol copolyester. In the preparation method, terephthalic acid or dimethyl terephthalate, 1,3-propanediol and ethylene glycol are used as raw materials, titanate, germanium compound and cobalt compound are used to form composite catalyst, phosphorus compound is added to be used as stabilizer; under the synergistic catalysis and hue-adjusting functions of the materials, the reaction time can be greatly shortened, the polyester chip of which intrinsic viscosity is 0.75-1.05dL/g is prepared through direct polymerization; and the reaction product has good hue, and the copolyester product can be used in the fields of fiber and engineering plastic.