The invention discloses a preparation method of multifunctional polyester fiber, and belongs to the technical field of preparation of functional materials and functional fiber. The preparation method comprises the following steps: 1, enabling functional metal ions to enter alpha-ZrP through ion exchange to form functional alpha-ZrP, then modifying the functional alpha-ZrP through KH550, acidifying a carbon material to obtain an acidified carbon material, modifying the acidified carbon material through an epoxy modifier E51 to obtain a modified carbon material, and adding the KH550-modified functional alpha-ZrP into the modified carbon material to form a multifunctional nanocluster; 2, blending and granulating the multifunctional nanocluster and a polyester matrix at 250 to 270 DEG C, then carrying out drying, and finally carrying out a melt spinning method to preparing the multifunctional polyester fiber by adopting a melt spinning method. The adding amount of an antibacterial object component in the multifunctional polyester fiber is small, and the antibacterial object component is uniformly dispersed; and the multifunctional polyester fiber has a persistent function, and the preparation method is easy and convenient to operate.