Aiming at the obvious trend of the contours on the high-altitude geomagnetic map, this paper presents a method of high-altitude geomagnetic matching area selection combining geomagnetic information entropy and geomagnetic direction entropy based on the study of geomagnetic information entropy and geomagnetic direction entropy. The method first uses geomagnetic information entropy to select the region with rich geomagnetic information, and then determines the direction of the flight trajectory according to geomagnetic direction entropy to obtain the optimal matching trajectory. Finally, the method compares and analyzes the matching localization results of three flight trajectories in different directions on the geomagnetic map at an altitude of 30,000 m by using semi-physical simulation. The experimental results show that the flight navigation error along the trajectory with small information entropy is small, and its positioning error is 12.7% of the trajectory positioning error along the maximum information entropy direction. Selecting the flight trajectory according to the value of the geomagnetic direction entropy can greatly improve the precision and reliability of the geomagnetic matching localization. The method in this paper can provide a basis for path planning of the geomagnetic matching navigation.