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Geomagnetic navigation needs matching areas with a good matching performance. Immunity particle swarm optimal (PSO) algorithm is used to select the optimal matching area intelligently in geomagnetic reference map, taking geomagnetic entropy as a characteristic parameter to measure the characteristic of each matching area. Mean square deviation (MSD) and normalized product (NProd) algorithms are both used in simulation experiments. Results indicate the consistency between matching probability and matching area selection policy, and the validity of characteristic parameter selection. This method can be useful in geomagnetic navigation.