In order to calibrate the non-orthogonal error and scale factor error of triaxial Helmholtz coil, a comprehensive error calibration method is proposed in this paper. The comprehensive error model is established first, and then the method to generate a frequency-controllable spatial rotating magnetic field whose magnetic field intensity is constant based on triaxial Helmholtz coil is introduced. Based on the fact that the magnetic field intensity generated by the current through the coil is constant, the objective function is constructed and the error parameters are solved using the least-squares fitting method. Simulation experiments and field tests prove the effectiveness and feasibility of this method. The most obvious finding to emerge from this study is that the proposed method is not only suitable for the electromagnetic shielding room environment but also suitable for the field tests in the presence of a background geomagnetic field far away from urban electricity interference. The root mean square error value is reduced to 0.7 nT from 298.2 nT in the electromagnetic shielding room, and it is reduced to 0.8 nT from 299.0 nT in the wild. Compared to the two-step calibration method, the proposed method reduces the sampling time by controlling the frequency of the rotating magnetic field and reduces the influence of the changes of the background geomagnetic field on the experimental results. This method has better anti-interference ability. Because the modulus of the background geomagnetic field has no effect on this method, it gets rid of the dependence on large current or background geomagnetic field shielding devices. Comparative experiments and repetitive experiments verify the practicability and stability of this method.