A real-time calibration method of magnetometer array’s misalignment errors with ac modulated three-axis coil

•An ac modulated three-axis coil calibrates misalignment errors of magnetometer array.•Varied currents of coils eliminate the necessity of non-magnetic rotation platform.•Ac responses of magnetometers are demodulated robustly with magnetic interferences.•Established theoretical model eliminates the necessity of total field magnetometer.•Errors of measured magnetic field gradient and localization decrease after the calibration.