Hard target penetration weapon is a trump card weapon for attacking multi-layered structural targets such as underground fortifications and command posts. The key to achieve the efficient damage to targets is the precise layer counting of fuse penetration process. Considering the oscillation aliasing and identifying difficulty in the traditional overload layer counting, a method of penetration layer counting based on the geomagnetic characteristic signal is proposed. During the warhead penetration of the reinforced concrete multilayer structure such as multi-story buildings, due to the additional magnetic field generated by magnetized ferromagnets in the geomagnetic field, the magnetic induction intensity measured by the sensor will change with its position related to the floors, so the layer can be counted by detecting the layer penetrating signal. The multi-layer target plate and warhead models are established, and the principle of penetration process, signal characteristics and layer counting strategy under the multi-parameter condition are analyzed through the COMSOL, a finite element analysis software. The purpose of this paper is to break through the large error and identifying difficulty of characteristic signals in the traditional layer counting method with accelerometer, and to provide theoretical reference for the design and damage efficiency improvement of penetration weapons.