Provided are ocean magnetic survey measurement method and system. The ocean magnetic survey measurement method includes a measuring operation for measuring an earth's magnetic field value using a magnetometer according to a heading angle of a probe, which is measured in clockwise direction on a basis of the true north, while the probe moves along a circular path based on a center point in an exploration target area with the magnetometer taken in tow, a data input operation for receiving, by a calculation unit, data for the heading angle of the probe and data for the earth's magnetic field value measured at the heading angle, a calculating operation for setting, by the calculation unit containing a calculation program therein, a magnetic disturbance value induced by the probe, which is included in the measured earth's magnetic field value, and calculating an actual earth's magnetic field value by subtracting the magnetic disturbance value from the measured earth's magnetic field value.