Abstract: Torreya grandis, a succulent shallow-rooted plant, is highly sensitive to soil moisture fluctuations. Short-term waterlogging induces root hypoxia, inhibiting growth or causing plant death, which limits its cultivation expansion and industrial benefits. To explore its physiological adaptation mechanisms to waterlogging, two-year-old T. grandis seedlings were subjected to normal watering (control) or waterlogging stress. We systematically analyzed the changes in root activity, oxidative damage indices, antioxidant enzyme activities, and osmotic adjustment substance contents, and combined untargeted metabolomics to identify key metabolic regulatory substances and differential metabolic pathways. The results showed that waterlogging stress significantly inhibited root activity in T. grandis, which is a key indicator of stress-induced growth inhibition. Physiologically, waterlogging triggered reactive oxygen species (ROS) accumulation, aggravated membrane lipid peroxidation, and increased electrolyte leakage, leading to severe oxidative damage in roots. In response, T. grandis roots activated the antioxidant defense system, upregulating SOD, POD and CAT activities to scavenge excess ROS, and accumulating proline and soluble sugars to regulate cellular osmotic pressure, thereby alleviating stress damage. Metabolomic analysis further revealed that waterlogging markedly affected root secondary and amino acid metabolism; flavonoid, terpenoid biosynthesis, as well as arginine and proline metabolic pathways were significantly activated, implying that metabolic network reconstruction may serve as a crucial adaptive mechanism. In conclusion, T. grandis seedlings mitigate waterlogging damage through the synergistic effects of antioxidant system activation, osmolyte accumulation and metabolic network reconstruction. This study clarifies the root activity variation pattern and physiological-metabolic response mechanisms under waterlogging stress, providing a theoretical basis for screening waterlogging-tolerant germplasm and breeding, and offering practical significance for stress-resistant cultivation and yield-quality improvement of T. grandis.