Comparative metabolomics is a powerful technique to unveil variabilities in metabolic composition between different plant types of the same species. Thus, unveiling the unique and common metabolites between plant types and unique medicinal properties has the potential to utilize the specific plant type in modern medicine. However, up to date, no study reports metabolite composition and medicinal properties of different color petiole types of Simarouba glauca (S. glauca), which is known for its potential pharmaceutical properties. In this study, we aimed to perform a metabolomic investigation on two different petiole types of S. glauca to unveil the unique and common metabolites and their therapeutic properties between these petiole plant types. In specific, we conducted a comprehensive metabolomic analysis of the green petiole (GP) and red petiole (RP) of S. glauca, that revealed 43 unique metabolites between both petiole types. The differentially accumulated metabolite analysis disclosed five differentially accumulated metabolites between RP and GP, in which two are highly accumulated in GP (4‐Amino‐1,5‐pentandioic acid and 2‐Myristynoyl pantetheine), and one (5‐Hydroxymethylfurfural) in RP. Furthermore, the chemical classification of identified metabolites resulted in 27 distinct chemical classes, with fatty acids and amino acids being notably enriched. Functional annotation highlighted the wound healing and antibacterial attributes of GP and the antipruritic and antiviral properties of RP. The pathway enrichment analysis revealed the involvement of the identified metabolites in cutin, suberin, and wax biosynthesis, along with fatty acid biosynthesis. Moreover, RP exhibited a higher abundance of anticancer metabolites compared to GP. Overall, the findings of this study offer valuable insights into the metabolic disparities, metabolite role in color variation, and medicinal potentials of different petiole types of S. glauca and underscore their promising pharmaceutical applications.