The invention provides a preparation method of functional polyester fibers. The preparation method mainly comprises the following two steps of: firstly, mixing functional powders, polybutylene terephthalate cyclic oligomer (CBT) and a dispersing agent, performing reactive extrusion on the mixture by double screws to prepare a polybutylene terephthalate (PBT) functional master batch, wherein the functional powders are one of or several of a carbon nano tube, nano titanium dioxide, tourmaline powders, a nano-silver antibacterial agent, a nano silicon oxide and fluorescent powders; and secondly, blending and spinning the master batch, the PBT, polyethylene glycol terephthalate (PET) or polytrimethylene terephthalate (PTT) to prepare the functional polyester fibers. According to the method, the reactive extrusion process is adopted, the operation is simple and convenient, the process flow is shortened greatly, the obtained PBT functional master batch contains 30wt%-40wt% of the functional powders, and can be well dispersed in a base body, the compatibility of the obtained functional master batch and polyester polymer is good, and the fiber obtained by the method has an obvious functional effect.