This paper proposes a ceramic ball/nylon elastomer composite structure. Experimental testing and finite element analysis were conducted to investigate the influence of key factors on the penetration resistance of the composite structures with constant total thickness. These factors include ceramic ball diameter, arrangement pattern, projectile head configuration, and the ratio of projectile diameter to ceramic ball diameter. The results indicate that the composite structures with three configurations exhibit higher resistance to round-nose projectiles compared to flat-nose projectiles. For projectiles with a diameter of 8.08mm (both round-nose and flat-nose), the composite structures with two-different-diameters ceramic balls exhibit better penetration resistance compared to those with single-diameter or triple-different-diameters ceramic balls. Furthermore, when the diameter ratio of the projectile to the front-layer ceramic balls falls within 0.73–1.01, the penetration resistance performance of the composite structure is relatively better, and optimal penetration resistance is achieved when the diameter ratio between the front-layer ceramic balls and other back-layer ceramic balls is 1.7–2.0. These findings provide valuable references for designing penetration-resistant protective structures for ships and other marine constructions.