Exogenous organic acids are beneficial in protecting plants from the stress of heavy metal toxins (e.g., Pb) in soils. This work focuses on the potential role of organic acids in protecting Changbai larch (Larix olgensis) seedlings from the stress of growing in nutrient deficient soil. The seedlings were planted in a nutrient rich or deficient soil (A1 horizon of a Haplic Cambisol without organic acid as the nutrient rich control, or fully-mixed A1 + B horizons in a proportion of 1:2 as deficient) in pots in a greenhouse. In A1 + B horizons the seedlings were treated daily with concentrations of oxalic or citric acid (OA or CA) at a rate approximately equivalent to 0, 0.04, 0.2, 1.0, or 2.0 mmol·kg−1 of soil for 10, 20, and 30 days. Nutrient deficiency stressed the seedlings as indicated by lipid peroxidation and malondialdehyde (MDA) content in leaves significantly increasing, and superoxide dismutase (SOD) activities, proline, photosynthetic pigment contents, and chlorophyll fluorescence (Fv/Fm) decreasing. The stress increased in controls over the application periods. When nutrient deficient plants were exposed to an organic acid (especially 5.0 or 10.0 mmol·L−1 for 20 days), the stress as indicated by the physiological parameters was reversed, and survival rate of seedlings, and biomass of root, stem, and leaf significantly increased; CA was more effective than OA. The results demonstrate that exogenous organic acids alleviate nutrient deficiency-induced oxidative injuries and improve the tolerance of L. olgensis seedlings to nutrient deficiency.