The integral equation method is widely used in ship′s magnetic field inversion modeling, but the model requires enough measurement points to obtain the ship′s magnetic field at a specific depth. To address the problem that the integral equation method uses the near-field magnetic field to model with poor accuracy, an improved measure by adding constraint equation was proposed. The numerical simulation of the magnetic field of a thin steel plate model and a 3D ship model was carried out respectively. The finite element method was used to initialize the selection of the ship′s internal measurement points. The inversion modeling was constructed based on the measured values of the internal magnetic field of the ship and the singular value decomposition method was used to solve the magnetic source parameters and predict the external space magnetic field. It shows that the root mean square error of the prediction results of the external space magnetic field of the ship is less than 12%. The magnetic field measurement experimental verification of the ship cabin model shows that the root mean square error of the prediction of the external magnetic field from the internal magnetic field of the cabin is about 13%, which proves the effectiveness of the proposed method and can improve the instability and insufficient accuracy of the traditional inversion model. The research results can provide ideas for the algorithm design of closed-loop degaussing of ships.