As an important civil and military infrastructure, airport runway pavement is faced up with threats from cluster munitions, since it is vulnerable to projectile impact with internal explosion. Aiming at the damage assessment of island airport runway pavement under impact, this work dealt with discrete modeling of rigid projectile penetration into concrete pavement and calcareous sand subgrade multi-layer structure. First, Discrete Element Method (DEM) is introduced to model concrete and calcareous sand granular material features like cohesive fracture and strain hardening due to compression, with mesoscale constitutive laws governing the normal and shear interactions between adjacent particles. Second, sequent DEM simulations of uniaxial and triaxial compression were performed to calibrate the DEM parameters for pavement concrete as well as subgrade calcareous sand. Piror to multi-layer structure investigations, penetration into sole concrete or calcareous sand is validated in terms of projectile deceleration and depth of penetration (DOP) with relative error