It is of extreme importance to develop a reliable numerical prediction technique to simulate the ballistic response of ceramic armor subjected to high-velocity impact (HVI) to economize the test cost and shorten the design period. In the present manuscript, a series of experiments on tungsten heavy alloy (WHA) fragment’s penetration into 99.5% alumina (AD995) armors are systematically simulated by employing the FE-converting-SPH technique. The numerical results are compared with the experimental counterparts to find that the FE-converting-SPH method is fairly efficient in predicting the depth of penetration, the residual velocity, length and mass of fragment, and reproducing the crack forms of ceramic. The applicability and accuracy of the numerical model in terms of the algorithm, material model parameters and contact definitions are validated. Then, the relevant parameters of the calibrated numerical model are incorporated to explore the influence of cover-layer thickness on the armor performance. A few mechanisms regarding the cover plate have been identified to act on the armor performance, such as the alteration of fracture cone half-angle, proportion of energy absorbed by ceramic, mushrooming deformation of fragment, etc. The result of multi-mechanism superposition is that the best ballistic performance is endued with 1 mm cover-layer armor, which demonstrates a 24.6% improvement over the bi-layer armor with 4.96 g/cm2area density, only at the cost of 15.7% increase in areal density, when back-plate thickness is held as 2 mm; for a constant area density of 4.96 g/cm2, a 1 mm cover-layer is also expected to be the best choice, with 10.7% improvement in armor performance.