The seed germination, seedling physiological and biochemical indexes of Polygala tenuifolia Willd. under drought stress were studied in this paper as the different PEG6000 treatments (2.5%-25%) were carried out in the experiments. The results showed that: (1) the initial germination time of P. tenuifolia seeds were delayed with the increasing of drought stress degree, and the seed germination rate, germination potential, germination index and vigor index were all decreased. However, the seed germination rate do not performance significant difference in 2.5%-15% PEG range compared to control while it significantly reduced under 20% PEG treatment (P<0.05). The seeds could not germinate absolutely at severe drought stress (25% PEG). The biomass and embryonic bud of P. tenuifolia were decreased, while the radical increased firstly and then decreased with the increasing of drought stress degree. (2) The seedling chlorophyll content increased with the increasing of treatment concentration and duration in 2.5%-10% PEG range, increasing firstly and then decreased at 15% and 20% PEG treatments. The highest chlorophyll content was observed in 10% PEG treatment at 15 days of P. tenuifolia, with 1.5 fold of the control. (3) The contents of free proline, soluble sugar and soluble protein continuously ascended with the increasing of treatment concentration and duration. The highest free proline, soluble sugar and soluble protein contents were recorded in the leaf tissue of P. tenuifolia at 15 days under 20% PEG treatment, with 1.99 fold, 1.53 fold and 1.50 fold of the control, respectively. (4) The activities of superoxide dismutase (SOD) and catalase (CAT) increased firstly and then decreased with the increasing of treatment duration, and the highest values of SOD and CAT activities were recorded in 10% PEG treatment at 10 days. The activity of peroxidase (POD) increased firstly and secondly decreased and finally increased, then decreased with the increasing of treatment duration, and the higher value of POD activity was recorded in 20% PEG treatment at 5 days. Malondialdehyde (MDA) content continuously ascended at 15% and 20% PEG solution, while increased firstly and then decreased in 2.5%-10% PEG range. The results demonstrated that the P. tenuifolia showed good adaptability to drought stress cause of the seeds could keep normal germination under light and moderate drought stress, and the seedlings could active adapt to drought stress environment by changing growth, osmotic substance content and antioxidant enzyme activity.