Pinus yunnanensis Franch., a vital forest resource in southwestern China, significantly impacting ecosystem stability and biodiversity. Variation of growth in height, a crucial trait for tree development, affects both yield and plant structure. Understanding this variation can enhance forest productivity and improve afforestation success. Although substantial differences in height growth are observed during the seedling stage of P.yunnanensis, the molecular mechanisms governing this variation remain unclear. In this study, more than 1900 P. yunnanensis seedlings in a homogenous garden were classified into three grades (I >
II >
III) using the mean ± ½ standard deviation method. The aim was to investigate the mechanisms underlying variation of growth in height during the rapid growth phase by analyzing phenotypic traits, nutrient elements, transcriptomics, and endogenous phytohormones. Results from the homogenous garden experiment revealed that the plant height and ground diameter growth of P. yunnanensis seedlings exhibited an S-shaped growth rhythm. The average nitrogen-to-phosphorus (N:P) ratio across organs was 3.97, indicating that nitrogen is the primary growth-limiting factor, with phosphorus also contributing to the limitation. Variations in nutrient content and stoichiometric ratios were found to significantly influence seedling height. Transcriptomic analysis highlighted significant enrichment in pathways including phenylpropanoid and flavonoid biosynthesis, and plant hormone signal transduction. A total of 22 endogenous phytohormones and metabolites were identified. The levels of IAA (indole-3-acetic acid), GA7 (gibberellin A7), and ABA (abscisic acid) followed the pattern: Grade I >
Grade II >
Grade III seedlings. Simultaneously, several candidate genes involved in plant hormone signal transduction were identified, including GH3, CYCD3, GID1, and others. These genes are involved in the biosynthesis pathways of auxins, brassinosteroids, and gibberellins, suggesting their role in regulating phytohormone levels and seedling height growth. This study provides comprehensive insights into variation of growth in height, laying the foundation for genetic improvement and effective cultivation of P. yunnanensis seedlings.