In response to the increasing threat of powerful earth-penetrating weapons, underground protective structures typically employ composite structural systems with reinforced steel layers. However, current numerical studies often simplify the entire structural system to plain concrete when assessing damage effects, and penetration and blasting processes are treated separately using a restart method. In this paper, we adopt an integrated simulation approach to analyze the resistance performance of composite protective structures with reinforcement layers. The results reveal significant differences in failure modes between plain concrete and reinforced concrete protective structures. The diameter of the steel bars and the spacing between mesh layers notably impact the penetration and blasting damage. Based on the results of a parameter analysis, we propose a method for optimizing the design of reinforcements in composite underground protective structures. The results of the study show the following: (1) The penetration and blast damage patterns of EPWs on plain concrete and composite protective structures with reinforcing mesh are significantly different. Compared to the plain concrete layer, the composite protection structure can effectively resist the damage of EPWs. (2) With the increase in reinforcement diameter, the decrease in reinforcement mesh spacing, and the increase in reinforcement dosage, the penetration depth gradually decreases; the amount and range of the blast damage also decrease accordingly. (3) Under the condition of the same reinforcement ratio, reducing the number of layers of reinforcement mesh, increasing the diameter of reinforcement, and configuring the reinforcement on the top of the protective structure as much as possible can improve the performance of the protective layer against penetration. At the same time, the reasonable arrangement of the reinforcement mesh can also enhance the ability of the protective structure to resist blasting damage.