The effect of the layer sequence on the ballistic performance of Ti6Al4V (35 mm)/CP-Ti (5 mm) laminated composite armor, against a 12.7 mm armor piercing projectile, was systematically investigated, both experimentally and computationally. By introducing the Johnson–Cook constitutive model and fracture criterion, the penetrating process of the composite plate was well-simulated. Furthermore, the influence of the layer sequence on the ballistic performance and failure mechanism of the composite plate was evaluated from the perspective of energy absorption and the stress distribution. Numerical simulation results of the macro morphology and penetration depth agreed well with the experimental results. The results showed that the energy absorption histories of each layer and stress distribution of the composite plate were found to be significantly affected by the arrangement sequence. The ballistic performance of Ti6Al4V/CP-Ti was far superior to that of CP-Ti/Ti6Al4V because more energy was absorbed in the early stage of the penetration process, thereby reducing the damage to the rear face. Further studies showed that the first principal stress in both structures was radially distributed in space, but was mainly concentrated at the rear face when the CP-Ti was placed at the front. Therefore, this stress induced cracking and failure in that region and, consequently, lowered the overall ballistic performance.