Abstract: The stored livestock manure is a major source of ammonia (NH₃) and hydrogen sulfide (H₂S), posing challenges to air quality and agricultural sustainability. Covering materials are an effective strategy for mitigating gas emissions during manure storage; however, conventional materials suffer from inadequate buoyancy, susceptibility to sedimentation, and limited adsorption capacity. To address these limitations, in this study, we developed a novel hydrophobic silica-modified expanded vermiculite (MV) for application in a swine liquid manure storage system. A systematic evaluation of odor (NH₃ and H₂S) reduction and environmental performance was conducted using three covering materials with 7 treatments: traditional woodchip, unmodified expanded vermiculite (V), and MV at 2 and 5 cm thicknesses, along with an uncovered control. Material characterization showed that MV surfaces were coated with fine particles, indicating successful adhesion of nanoscale hydrophobic silica. MV exhibited enhanced hydrophobicity (water contact angle > 102°) and a higher specific surface area (12.34 m²∙g⁻¹) compared to V (5.64 m²∙g⁻¹), confirming its transformation into a composite material with improved floatation and adsorption properties than those of V. MV treatments significantly reduced NH₃ emissions by 87%–95% compared to the control. Compared to V, MV improved NH₃ reduction efficiency by 53%–93%, although it had no significant effect on H₂S emissions. Notably, MV treatments preserved ammonium nitrogen content with 23%–28% greater efficacy than the uncovered treatment, due to its combined gas adsorption and physical barrier mechanisms. Mantel test results highlighted the importance of maintaining material buoyancy to control NH₃ and H₂S emissions. MV’s good floatation prevents submersion and enables effective NH₃ reduction and H₂S adsorption, avoiding the H₂S emission increases observed with traditional covers. Contrastingly, V and woodchip covers tended to sink, failed to form stable layers, and could increase gas emissions by introducing nutrients or sulfur sources into the manure. Life-cycle assessment showed that MV had superior environmental performance, reducing total environmental cost by 98.0% relative to the control, largely due to its high NH₃ mitigation potential. The abatement cost of MV was CNY 1 054 per year — an 82.7% reduction compared to V (CNY 6 113 per year). This improved performance is attributed to MV’s buoyancy and chemical stability, which suppress gas diffusion and maintain structural durability during long-term storage. In summary, the hydrophobic MV developed in this study effectively reduces NH₃ emissions, preserves ammonium nitrogen, and has no adverse impact on H₂S emissions during manure storage. It offers both environmental and economic benefits, making it a promising, safe, and cost-effective covering material for livestock manure management. This research provides a novel approach and theoretical basis for reducing gas emissions during manure storage.