This article is about compensating for the effect of underwater magnetic carrier. Using the dragging type magnetometer(G882) to measure in the water's field, and calculating the 3 components of magnetic field according the measuring result, geomagnetic inclination and geomagnetic declination, and then establishing a compensating model. And then according another result (measured by the CS-L which is combined with the carrier) putting all the 2 data into the theory compensating equation to get the compensating coefficient. For now, the real compensating equation for the experimental water has been come out. Using both of the 2 types of magnetometers to survey in the other open water field, 2 groups of the newly measured data can be obtained. To substitute data (obtained by Cs-l) into the real newly established equation, the compensated data of the water field have been calculated. Then drawing a figure which contained all the 3 kinds of data together, the result of this compensation can be observed. From the figure, the reliability of this compensation's way has been verified. This sort of approach is a better way to reduce the interference caused by the carrier when the magnetometer is combined with the carrier and to widening the applied range for the way of reducing the interference caused by the carrier.