Abstract: Allometric growthcan reflect the relationship between plant organs and fertilizer treatments. To explore the growth response of Pinus yunnanensis Franch. seedlings to fertilizer application after stubble leveling from the perspective of nitrogen(N) and phosphorus(P) rationing, and to analyze the growth rate of biomass of P. yunnanensis organs through anisotropic growth. To this end, this study used a three-level 3 × 3 regression design with two factors of N and P to conduct a fertilization experiment on 1-year-old P. yunnanensis seedlings after stubble leveling and explored the growth relationships between each organ and sprout, between each organ and root biomass, and between each organ and individual size. The results showed that the combined application of N and P fertilizers led to higher variability in biomass among different organs. After decapitating, there was a significant allometric growth relationship between various organs and shoots of P. yunnanensis seedlings: most changes in needles-shoot allometry were not affected by variations in N and P fertilization; however, root-shoot and stem-shoot allometric curves changed, indicating that different levels of N and P fertilization would have varying effects on the growth of P. yunnanensis seedlings after decapitating. Under different N and P fertilization treatments, different allometric growth patterns were observed among various organs, with the majority showing an allometric growth relationship. In conclusion, the allometric growth relationship among various organs of P. yunnanensis seedlings after decapitating is influenced by fertilizer application, especially altering the shoot-allometry relationship with other organs. Most treatments exhibited an allometric growth relationship between roots, stems, aboveground parts and shoots with a slope close to or less than 0.500. Additionally, fertilizer application promoted biomass accumulation in various organs and accelerated seedling growth rate.