Secondary fragments formed by the projectile core penetrating the target plate are closely related to the accurately evaluation of the damage effectiveness. To address the problem of unclear characteristics of secondary fragments, a search reconstruction algorithm for secondary fragments is established in this paper. First, the penetration process is numerically simulated to obtain all the particles that can characterize the secondary fragments. Then, non-independence matrices reflecting the interactions among all particles are constructed. Finally, all the fragments are screened according to the non-independence matrix to obtain the number of fragments and the mass, volume, velocity, center-of-mass coordinates of each fragment. As verified by the penetration test, the search reconstruction algorithm proposed in this paper is capable of accurately characterizing the secondary fragments while taking into account the computational efficiency. In addition, it can be seen from the penetration test and simulation results that at 0.6m from the target plate, the scattering radii of the secondary fragments are basically the same for different initial velocities of the projectile core, and the same is true at 1.4m from the target plate. The damage mode of the irregular fragments formed by the projectile core penetrating the target plate on the fiber layer in the bulletproof vest is dominated by shear damage. As the velocity of the fragments decreases, the corresponding shear effect is weakened, and the fiber layer produces strong tensile deformation, the vest appears to bend and delamination phenomenon. With the initial velocity of the projectile core increasing, the greater the deformation of the projectile core after penetrating the target plate. The more fragments produced by the projectile core, the smaller the average mass and the less volume of the fragments. The radial velocity of the fragments increases with the increase of the initial velocity of the projectile core, and the scattering radius of the fragments shows the same trend.