The seeds of Glycyrrhiza uralensis Fisch. used for cultivating are primarily sourced from wild populations. However, the types of habitats where wild G. uralensis grow are diverse. We studied the effects of salinity on the growth, antioxidant capacity, and photosynthetic physiology of two-month-old licorice seedlings from different habitats to evaluate their salt tolerance. With the increasing NaCl concentration, compared with non-salinized habitats, seedlings originating from seeds collected from salinized habitats showed milder inhibition in root biomass and root volume. Also, the crown diameter increased more significantly. Activities of superoxide dismutase, catalase, and peroxidase are higher. Correspondingly, the electrolyte leakage rate of the leaves is low. Their leaves had a higher photoprotection capacity and potential maximum photochemical efficiency of PSII. Net photosynthetic rate, transpiration rate, and stomatal conductance showed less inhibition under 4 and 6 g/kg NaCl treatment. The content of glycyrrhizic acid and glycyrrhetinic acid in their roots was significantly increased under 2 g/kg NaCl treatment and was significantly higher than that of seedlings from non-salinized habitats under the same NaCl treatment. In conclusion, seeds from salinized habitats show improved tolerance to salt stress at the seedling stage, which is attributed to their superior phenotypic adaptability, strong antioxidant, and especially high light protection ability.