A geomagnetic sensor for auto-calibration of a deviation and a method of using the geomagnetic sensor. The geomagnetic sensor includes a geomagnetic detector including X-axis and Y-axis fluxgates orthogonal to each other and receiving a drive signal to detect an electromotive force corresponding to a geomagnetism, a signal processor converting the electromotive force output from the geomagnetic detector into X-axis and Y-axis output values and outputting the X-axis and Y-axis output values, and a drive signal generator applying the drive signal to the geomagnetic detector. Each of the X-axis and Y-axis fluxgates includes cores, a solenoid type exciting coil, and at least two detection coils winding around the cores in a solenoid form. Accordingly, as an azimuth is measured using output values detected by the separated detection coil, the azimuth can be exactly and easily detected regardless of an external magnetic field.