Objective To analyze the main metabolites and their relative contents in leaves, shoots, fruits and barks of Mahogany by non-targeted metabonomics, so as to provide a scientific basis for improving the medicinal value of Mahogany. Methods High performance liquid chromatography-mass spectrometry (HPLC-MS) was used to collect the data of metabolites in different parts of Mahogany, and then the main metabolites were analyzed by non-targeted metabonomics. The results showed that leaves, twigs, fruits and barks all contained flavonoids, benzene and its substituted derivatives, carboxylic acids and their derivatives, fatty acids, phenylpropanoids and other metabolites, with the highest content of flavonoids in leaves and the richest content of carboxylic acids and their derivatives in fruits. The main metabolic pathways of fruit and bark are amino acid metabolism, flavonoids biosynthesis, flavonoids and flavonols biosynthesis. Conclusion The leaves, twigs, fruits and barks of Mahogany contain a variety of metabolites with medicinal functions, and the highest content of metabolites is found in different parts. Therefore, targeted collection of medicinal parts can be considered in the development and utilization to improve the utilization rate of resources.