Tropical fruits are essential for the macronutrient and micronutrient needs of a person. A comprehensive understanding of the nutrients or compounds from tropical fruits could elucidate the benefits more deeply and unlock potential for future health. Gas chromatography-mass spectrometer (GC-MS) analysis is an important instrument for analyzing comprehensive metabolites, also known as metabolomics, from samples, including tropical fruits. However, several metabolites need to be separated and also derivatized to ensure their ability to be detected by GC-MS. Therefore, proper extraction and derivatization methods are crucial to give clarity to the produced result. This book chapter explains about the method used in several research paper of GC-MS tropical fruits analysis that use Bligh-Dyer method-base extraction and double derivatization steps from oximation and silylation. Using a combination of these steps, these research can detect more than 50 metabolites from several classes, such as amino acids, sugars, sugar alcohols, organic acids, etc. Therefore, the detailed materials, methods, and notes acquired from experience are hoped to help other tropical fruit researchers to perform GC-MS analysis in the future.