The invention discloses a phase sequence arrangement adjustment method for three-phase current unbalanced wires of transmission lines in a transformer substation to solve the problem that the three-phase current unbalance degree of existing transmission lines is increased, and therefore misoperation frequently occurs during zero-sequence protection for buses and the transmission lines of the transformer substation. The method include the steps of firstly, setting up an unbalance current simulating calculation model of all the connected transmission lines according to the types of towers used for all the transmission lines of the whole transformer substation, the phase sequence arrangement of all the transmission lines and the actual lengths of the transmission lines; secondly, calculating a positive-sequence current, a negative-sequence current and a zero-sequence current of each transmission line of the whole transformer substation and the zero-sequence current unbalance degree and the negative-sequence current unbalance degree of each transmission line. By changing the phase sequence arrangement of the wires of the transmission lines, the zero-sequence current unbalance degree and the negative-sequence current unbalance degree of each transmission line are controlled below 5% until the zero-sequence current unbalance degrees and the negative-sequence current unbalance degrees of all the transmission lines of the transformer substation are calculated to be lower than 5%. The simple and practical adjustment method is provided for the optimal phase sequence arrangement of the wires of all the transmission lines of the transformer substation.