The invention discloses a segmented polyester copolymer and a preparation method thereof. A structural formula of the copolymer is shown as a formula (I). An organic catalyst is directly adopted, so that the steps are simple and convenient in a polymer purification process, and heavy metal ions in a conventional method cannot be remained in a polymer. The esterification reaction of acid anhydride and an epoxy compound can be selectively catalyzed to obtain the polyester copolymer with geometrical isomerism chain segments, and generation of byproducts caused by catalysis of the open-loop auto-polymerization reaction of an epoxy group is avoided by the nuclear magnetic analysis of products.