The invention discloses a method for preparing ultra-fine denier skin-affinity polyester filaments. The method comprises the steps of POY precursors, pre-interlace, first feeding roller, first deformation heat box, cooling plate, false twister, second feeding roller, intermediate interlace, second heat box, third feeding roller, oiling roller, DTY winding shaping and spinning cake inspection, wherein the intermediate interlace procedure can be removed, the temperature of the first deformation heat box is 165 DEG C-175 DEG C, the temperature of the second heat box is 130 DEG C-140 DEG C, the draft ratio is 1.58-1.68, the false twist ratio is 1.66-1.80, and the interlace air pressure is 0.03-0.15 MPA. The method has the advantages of being simple and easy to operate, fabric prepared by polyester filaments prepared by means of the method has the advantages of being more flexible, good in comfort performance and strong in visual and tactile feeling.