Hydrogen gas (H2) is considered as a signaling molecule and plays multiple roles in plant growth. However, the effect of H2 on postharvest physiology in lily scales during storage has not been reported. In this study, the regulatory roles of hydrogen-rich water (HRW, a H2 donor, a concentration of 0.45 mM for 100% HRW) in water status, ion balance, and nutrients in Lanzhou lily (Lilium davidii var. unicolor) scales were investigated. The scales were soaked in HRW for 12 d, and sampling was performed every 3 d for a total of 5 times. The results show that HRW (0, 10, 50, and 100%) increased the fresh weight, dry weight, relative water content, and water loss rate in lily scales, with maximum biological response at 50% HRW. Treatment with 50% HRW significantly increased the K+ content and K+/Na+ ratio in lily scales and decreased Na+ content. The Na+ K+-ATPase, and PM H+-ATPase activities were also increased by 50% HRW treatment. Meanwhile, 50% HRW up-regulated the expression of AKT1 and HA3 genes and down-regulated the expression of NHX2 and SOS1 genes. In addition, 50% HRW treatment significantly increased the expression level of PIP1;5, PIP2A, TIP1;3, and TIP2;2 genes. Treatment with 50% HRW significantly increased the content of water-soluble carbohydrate, sucrose, glucose, and fructose in lily scales, and decreased the content of starch. In addition, 50% HRW treatment significantly increased the activity of α-amylase, β-amylase, total amylase, sucrose synthase, and sucrose phosphate synthase. Collectively, H2 might enhance the water retention capacity and nutrient content in lily scales by maintaining ion balance, regulating aquaporin, and increasing sugar-metabolizing enzyme activity, thereby prolonging the storage period of postharvest scales of Lanzhou lily.