Impermeability and durability constrain the application of permanent shotcrete lining. Silane is commonly used in the field of concrete waterproofing. However, the silane material alone affects the strength of concrete. Zeolite powder has a certain activity and is a good natural carrier. Therefore, this study utilized Isobutyltriethoxysilane-Zeolite powder (IBTES-ZP) to address the impermeability of shotcrete, the mechanism of impermeability, and practical application. The water absorption, compressive strength, and impermeability properties of the IBTES-ZP-incorporated and unadmixed conditions were analyzed experimentally, and the micromechanisms were explored by contact angle testing (CA), X-ray diffraction (XRD), thermogravimetric analysis (TGA), scanning electron microscopy (SEM), and mercury intrusion analysis (MIP). The results showed that the admixture of IBTES-ZP had an unfavorable effect on the early compressive strength of shotcrete, but the 28-d strength was higher than that of unadulterated shotcrete when the admixture was up to 7.5%. IBTES-ZP reduced the capillary water absorption of concrete and realized overall water-repellent properties to a certain extent, improved the water penetration and chloride migration resistance compared with those of the blank group, and reached the optimal value at dosages between 5% and 7.5%. Microanalysis revealed that IBTES-ZP retarded early hydration and promoted late hydration. The active substance of zeolite powder in the capillary pores and the cement hydration product Ca(OH)2 in the alkali-free liquid accelerator and gypsum under the action of the secondary hydration reaction generated calcium alumina (AFt) crystals and hydrated calcium silicate (C-S-H) gels, reduced the pore volume and enhanced internal densification. Field application shows that IBTES-ZP at a dosage of 5% can effectively enhance the impermeability of shotcrete single-layer lining structures. This study provides a reference for the application of shotcrete materials with waterproofing properties in the permanent single-layer lining of tunnels.