The invention relates to an underwater carrier geomagnetic three-component measuring method. A geomagnetic three-component value of a point without a magnetic anomaly is measured by making a nonmagnetic carrier carry a three-component magnetometer in a known area; then, a pair of three-component magnetometers is carried by a magnetic carrier, relevant parameters of sensor locations are obtained through solution; next, magnetic field three-component values with interference in an unknown area are measured according to measuring lines; an external interfering magnetic field is removed through difference, and an underwater geomagnetic vector diagram is drawn according to the obtained geomagnetic field three-component values in the unknown area. Compared with the method of satellite measurement or water surface measurement downward continuation, underwater geomagnetic field data obtained through the underwater carrier geomagnetic three-component measuring method are more reliable and more authentic, the underwater carrier geomagnetic three-component measuring method accords with geomagnetic characteristics of underwater on-site environments, and the measurement data are valid for a long time. The geomagnetic field three-component measurement accuracy is improved, the anti-jamming capability is enhanced, and accurate geomagnetic three-component measurement of an underwater carrier is realized. The underwater carrier geomagnetic three-component measuring method is applicable to compensation for influences of a ground carrier, an aerial carrier and the underwater carrier on geomagnetic field component measurement, in particular to geomagnetic navigation of the carriers.