To solve the problem that the magnetic field distribution of submarine at high altitude is difficult to measure in aeromagnetic anomaly detection, the Maxwell equation set and the boundary elements method are taken into consideration. According to the Green function and the distribution of vector potential, the spatial distribution of magnetic field of submarine is obtained in the prediction space, and the prediction model of submarine magnetic field is established. By using the magnetic dipole to simulate the submarine target, the prediction model is validated preliminarily in theory. Further more, an experiment is designed to verify the effectiveness of the prediction model.The results of the theoretical test and experimental verification show that the mean absolute error and the mean relative error of the submarine magnetic field prediction model using boundary elements method are respectively 0.220 5 nT and 2.368%.