Phoebe bournei is a rare and endangered woody species and the success of its plantation development is dependent upon proper seedling cultivation. This study explored the regulation of N, P and K fertilizer and the interaction of these macronutrients on the growth of Phoebe bournei seedlings. To determine the optimum rate and ratio of N–P–K fertilizer in seedling cultivation, we used the unique “3414” incomplete orthogonal regression design to evaluate the effects of N–P–K fertilization on seedling morphological development. One-year-old Phoebe bournei bareroot seedlings were grown for one growing season under the defined fertilization regime, with their morphological development determined by measuring seedling attributes—root, stem, leaves and total biomass, root collar diameter and seedling height. These attributes were then combined to calculate the following indices: height-diameter ratio, shoot-root ratio and the seedling quality index (QI). Results showed that the N–P–K fertilizer had significant and beneficial effect on seedling cultivation. N effect was highest, followed by K and P. The three-way N×P×K interaction effect was strong, and the two-way interactions effect was highest for N×P, followed by P×K and N×K. At the “2” level of N (0.532 g·plant−1), P (P2O5, 0.133 g·plant−1), and K fertilizer (K2O, 0.356 g·plant−1), seedling growth and biomass accumulation were at their maximum. Unary, binary, and ternary quadratic fertilizer effect function equations of QI were established. Through comparative analysis, the ternary quadratic model was the optimal model and through a simulation–optimization, the optimal N–P–K fertilizer rates were 0.373~0.420 g·plant−1 (N), 0.086~0.106 g·plant−1 (P2O5), 0.243~0.280 g·plant−1 (K2O), with a N–P–K ratio of 1:0.20:0.43~1:0.65:0.75.

To study the effect of N-P-K fertilization on Phoebe bournei seedlings’ organs dry biomass, and nutrients accumulation and allocation, and to further uncover how nutrients regulating dry biomass formation through fertilization, we utilized the “3414” experiment design. The results showed that N, P, and K fertilizer promoted dry biomass accumulation, and root, stem, and total plant N, P, and K content and accumulation in seedlings. The dry biomass accumulations of root, stem, and total plant increased first and then decreased with the increase of N, P, and K application rates, which was basically consistent with the change in dry biomass allocations and N, P, and K contents, accumulations, and allocations. Root N accumulation, root P accumulation, and total plant K accumulation were the key indicators for seedlings growth. N fertilizer had the greatest effect on total dry biomass and root N accumulation, was the most important fertilizer for the growth of Phoebe bournei seedlings, can regulate the growth of root and leaves, is beneficial to root growth at medium-low N fertilizer levels (N: 0.266–0.532 g·plant−1), and leaves growth at high N fertilizer level (N: 0.798 g·plant−1). P fertilizer rate can regulate the seedling stem growth, reaching the maximum at the medium level P application (P2O5: 0.1332 g·plant−1). K fertilizer had the greatest effect on the root P accumulation and total K accumulation, promoting K transport from leaves to root, improved root and stem growth, and inhibited leaves growth. The N, P, and K fertilizer three-factor application can better promote nutrient uptake than double-factor and single-factor fertilization, with highest dry biomass accumulation at the medium level of N, P, K fertilizer (N: 0.532 g·plant−1; P2O5: 0.1232 g·plant−1; K2O: 0.356 g·plant−1). In conclusion, N, P, and K fertilization promoted the N, P, and K absorption, increased root, stem, and leaves N, P, and K content and accumulation, and promoted the seedling dry biomass accumulation, but reversed under excessive application of N, P, and K fertilizer; and N fertilizer was beneficial to root and leaves growth, P fertilizer to stem growth, and K fertilizer to material transfer, which provided a theoretical basis for robust Phoebe bournei seedling cultivation.