The invention relates to an orthogonal field calibration device for a three-component magnetic probe and a calibration method thereof. The device is formed in a way that a thrust bearing and more than three stop blocks are arranged on a base; the stop blocks are used for limiting a rotary platform; the rotary platform is arranged on the thrust bearing; a cylinder is fixed on the rotary platform; the upper part of the cylinder is provided with two ear-shaped raised lines; a horizontal shaft coincides with a disk in diameter and is fixed on the disk; both ends of the horizontal shaft respectively pass through the two ear-shaped raised lines; the disk is hung between the two ear-shaped raised lines; the disk rotates around the horizontal shaft; the disk is provided with an angle scale; a three-component probe is fixed on the angle scale through a bolt or a rotary shaft; and one end of the three-component probe is provided with a connector. The device can completely ensure that three non-orthogonal magnetic probe sensitive shafts scan through a total space equiprobably as much as possible in the measurement process. The calibration device has a simple structure and low cost, and a special calibration environment is not needed, thereby, the measurement cost is greatly reduced, the fieldwork is facilitated, and the measurement efficiency is improved.