A void in a tunnel’s secondary lining vault endangers traffic safety, as it affects the mechanical properties and the durability of a tunnel’s structure. In this paper, the damage due to a void and the repair effect of mold grouting were studied. In order to consider the contact effect of the waterproof layer, an interface element was used to connect the secondary lining and the primary lining, and the connection stiffness was limited. On this basis, the effect of a void on the mechanical behavior of the secondary lining was studied by numerical simulation. Then, a numerical model of the contact surface between the grouting body and the molded concrete was established and combined with a typical tunnel model. By changing the bonding strength of the contact surface, the relationship between the mechanical behavior of the grouting body and its bonding performance was analyzed, and its influence on the whole lining is discussed. Finally, the effect of mold grouting is discussed on the basis of field tests and the monitoring results. The results showed that the risk of a crack or even failure of the secondary lining increases significantly with the expansion of a void. Considering the contact effect of the waterproof layer, the connection stiffness between the secondary lining and the primary lining was significantly reduced, and the secondary lining showed more obvious independence and integrity. The insufficiency of the bonding strength between the grouting body and the molded concrete led to the loss of shear strength, and the failure would start from the edge of the grouting body and develop toward the middle. In the cases of class III, IV, and V surrounding rock, the recommended shear strength of the contact surface is about 0.65 MPa, 0.85 MPa, and 1.10 MPa, respectively. The construction method of the mold grouting can guarantee the effective bonding between a grouting body and the molded concrete, so as to avoid cracks, block falling, collapse, and other damage.