An improved total field calibration system and method is disclosed for reducing the rotational misalignment between magnetic and gravity sensors in a directional sensing system. A method of calibrating a tri-axial directional sensor comprising orthonormal accelerometers and orthonormal magnetometers, comprises measuring Earth's magnetic and gravity fields with said directional sensor in at least 4 sensor orientations; obtaining at least one reference field value of dip drift of Earth's magnetic field from at least one source independent of said directional sensor corresponding to said orientations; and, determining and applying rotational misalignments between said magnetometers and said accelerometers so that measured magnetic dip drifts are substantially equal to said reference values. The calibration process can be performed without monitoring the declination change during the calibration process. Directional sensing systems can be calibrated accurately during a period when the Earth's magnetic field changes rapidly.