Introduction Plants adapt to different environmental conditions through resource allocation and optimization across different organs (leaves, stems, and roots). Across different ecosystems or communities, these organs may coordinate, trade off, or operate independently to adapt to habitat environmental conditions. However, in rocky desertification habitats, the specific inter-organ relationships during resource allocation and optimization remain unclear due to limited research.Methods This study examined 30 trait characteristics of leaves, stems, and fine roots of Pseudotsuga sinensis, a tree species adapted to rocky desertification environments, to investigate the associations among organs.Results Principal component analysis (PCA) revealed that leaf traits were structured along orthogonal axes representing defense (PCA 1) and nutrient strategy (PCA 2). Stem traits were organized along axes related to water acquisition and transport (PCA 1) and nutrient strategy (PCA 2), while fine root traits aligned with defense (PCA 1) and nutrient strategy (PCA 2). Correlation analysis indicated a significant negative relationship between leaves and fine roots in Pseudotsuga sinensis, suggesting a trade-off in defense investment between these organs in response to rocky desertification conditions. Non-significant correlations between stems and roots, as well as between leaves and stems, imply independent defense and resource strategies in these organs.Conclusions The findings revealed that the linkage mechanisms and strategies between leaves and roots in plants adapting to rocky desertification habitats, provide insights for the restoration and management of rocky desertification areas.