Abstract: Taxus wallichiana var. mairei, a nationally protected Class Ⅰ wild plant in China, holds significant medicinal and ornamental value. Optimizing water and nutrient input during early vegetative growth is critical for successful seedling cultivation. This study evaluated the effects of different water and fertilizer management strategies on the morphological and physiological performance of T. wallichiana var. mairei seedlings. Seedling responses to water-fertilizer interactions were assessed using integrated statistical analyses. In comparison to other treatments, the combination of 60% irrigation volume with 1.5 kg/m³ slow-release fertilizer was most conducive to T. wallichiana var. mairei seedling growth. Compared with the control, aboveground, belowground, and total biomass increased by 116.36%, 178.71%, and 133.18%, respectively, while seedling height, basal diameter, root surface area, and root length increased by 53.14%, 64.60%, 166.37%, and 142.51%, respectively. Significant improvements in chlorophyll, soluble sugar, and soluble protein content were also observed. These findings support the implementation of 60% irrigation coupled with 1.5 kg/m³ slow-release fertilization to enhance early-stage growth in T. wallichiana var. mairei seedling propagation.