It is possible to suppress core misalignment from occurring due to relative vibration between a cutting tool and a workpiece, to improve accuracy of a finished shape, and to suppress a tip of the cutting tool from being influenced. A numerical controller that causes a machine tool to perform an operation for performing thread cutting through which a cutting tool and a machining target are allowed to move relative to each other to perform cutting-in processes a plurality of times on the machining target to form a thread on the machining target, including: a driver that controls a spindle that rotates the machining target, and drive axes having three axes; a vibration superimposing unit that superimposes vibration to be applied to two axes or more among the three axes on the relative movement between the cutting tool and the machining target so that the cutting tool and the machining target vibrate relative to each other along a thread groove; and a thread cutting vibration adjusting unit that shifts, by a vibration phase shift amount set beforehand, a phase of the vibration relative to a phase of the spindle per each of the cutting-in processes to be performed the plurality of times.