Summary Plant functional traits are important to understanding biodiversity and ecosystem functioning responses to global change. However, traditional plant trait network (PTN) theory does not adequately capture coordinated adjustment mechanisms operating among traits across multiple organs and functional systems. To address this challenge, we introduce the use of plant trait multilayer networks (PTMNs). This innovative framework systematically integrates multilayer network theory with plant functional trait analysis, enabling quantitative assessments of trait relationships across plant organs and functional systems. We applied both traditional PTN and PTMN analyses to a dataset of 76 native and non‐native woody species in North American deciduous forests, examining relationships among leaf, stem, and root traits. PTN results showed that non‐native species already displayed higher connectivity and integration within single‐layer networks, while PTMN analysis further revealed stronger cross‐layer links and more efficient coordination across multiple organs and functional systems, indicating enhanced integrative capacity and adjustment potential in non‐native species. In conclusion, by analyzing trait interdependencies across organs and functional systems, PTMNs provide a comprehensive framework for understanding the complex ways plants respond to environmental change, thereby enhancing predictions of biodiversity patterns and ecosystem resilience.