Wild Glycyrrhiza uralensis Fisch. populations have diverse habitats, and seeds from different habitats are often mixed for cultivation. However, differences in the responses of seeds from different habitats to soil moisture conditions at the germination and seedling growth stages are unclear. We compared the response of seed germination and seedling growth, yield, and quality of medicinal materials from saline and non-saline populations with different water supplies. The seed germination stage was more tolerant to drought in non-saline compared to saline populations. Seedlings from saline populations showed the highest net photosynthetic rate, biomass of roots, stems, and leaves, and glycyrrhetinic acid content in roots under high water treatment. Following low water treatment, glabridin showed the highest content, and the net photosynthetic rate, biomass, and other medicinal components were significantly decreased. Under high water treatment, the glycyrrhizic acid, liquiritin, liquiritigenin, isoliquiritigenin, glabridin, and total flavonoid contents in non-saline population seedlings were highest among all treatment groups; the opposite results were observed under low water conditions. Therefore, to optimize the yield of medicinal material yield and glycyrrhetinic acid content, seeds from saline populations with sufficient water should be selected. Although the root biomass of non-saline populations did not significantly differ under the two water supply conditions, the contents of glycyrrhizic acid, liquiritin, liquiritigenin, isoliquiritigenin, glabridin and total flavonoids in the roots were significantly higher in the high than in the low water treatment group. During liquorice cultivation, an adequate water supply is necessary, and seeds from the two populations should be collected and sold separately.