Aiming at the problems of low accuracy and low adaptability of the existing ship magnetic field inversion modeling methods with equivalent sources, a new method of inversion modeling of magnetic monopole array of ship magnetic fields is proposed. Three-dimensional ship magnetic monopole array is arranged according to the ship ferromagnetic structure, and the inversion prediction model of ship magnetic fields is established by regularization technology. Three typical forms of magnetic monopole arrays are established: rectangular magnetic monopole array on the horizontal surface of the draft line, cuboid magnetic monopole array enclosing the ship hull, three-dimensional ship magnetic monopole array distributed according to the ship’s ferromagnetic structure. The theoretical analysis shows that the three-dimensional ship magnetic monopole array reduces the blindness of the equivalent magnetic source setting, and the obtained equivalent magnetic source is highly consistent with the real magnetic source, which can reproduce the complete magnetic field information of the ship to a greater extent. The magnetic field of a typical virtual ship is applied to the validation test. The results show that the proposed three-dimensional ship magnetic monopole array has higher precision and adaptability than the rectangular or cuboid magnetic monopole array. In particular, the proposed three-dimensional ship magnetic monopole array can realize the mutual conversion between the near and far magnetic fields, and between the magnetic fields above and below the ship. The proposed three-dimensional ship magnetic monopole array model has the unique advantages of small complexity, simple modeling and flexible layout, and it provides an alternative method for the high-precision data processing and explanation to the inversion modeling of ship magnetic fields, ship magnetic field positioning, et al.