Based on the equivalent transformation of measurement model and geometric meaning, an equivalent twostep algorithm is proposed for the calibration of threeaxis magnetic sensor. The calibration is divided into two steps: the equivalent sensor frame calibration and the equivalent misalignment calibration. The significance and characteristics of the equivalent transformation analysis method are described in the study. The calculation formula of the parameters in the equivalent sensor coordinate system is derived and the geometric meaning of parameters calibrated by the ellipsoid method is defined. The principal component analysis is utlized in the equivalent misalignment calibration, correspondingly, the sign inversion and nonorthogonality defects are analyzed as well as; the correction algorithms are studied. The equivalent twostep algorithm can calibrate threeaxis magnetic sensor without external attitude information, geomagnetic information and auxiliary sensors. Experiments show that its calibration accuracy is close to that of dot product invariance algorithm.