With the development of underwater detection and communication technology, the traditional magnetic measurement model cannot meet the requirements for high precision and high efficiency modeling. In order to solve this problem, according to the integral model of ship magnetic field, we comprehensively analyze the discretization error caused by the composite middle rectangular and Gauss-Legendre integral remainders generated by discretizing the integral model into the magnetic dipole array model, the algorithm error, the fitting error caused by the model simplification, the model error, etc. and we also use these research results to analyze the model applicability conditions. Then based on the correlation between model error and parameters as well as accuracy and computational complexity, the multi-objective optimization problem is constructed. The NSGA-II algorithm is used to solve the multi-objective function, and the optimal solution set with balanced accuracy and complexity is obtained. The selection rules under the different requirements for accuracy and complexity are proposed. In order to ensure the effectiveness of the results, the model is simulated by using the actual submarine data on the basis of the hybrid model of ship magnetic field. The relationship between the distance to reach the applicable range of the model and the number of magnetic dipoles is obtained through the simulation analysis of the submarines with uniform and nonuniform magnetic field, and the simulation results are compared with the existing research results to ensure the effectiveness of the simulation results. At the same time, under the condition of ensuring the applicability of the model, the results obtained in the multi-objective optimization process based on NSGA-II algorithm are of high computational efficiency and accuracy. Therefore, this method has good engineering application value.