Miso is a traditional fermented food that represents Japan, and its unique flavor and functionality are due to the presence of various metabolites. In this chapter, we introduce the gas chromatography-mass spectrometry (GC-MS) analysis method with the aim of comprehensively clarifying the overall picture of the nonvolatile flavor components that make up miso. GC-MS can be used to analyze nonvolatile components through derivatization and to extract molecules that contribute to the aroma of miso. This method enables the identification and profiling of metabolites characteristic of miso. This chapter describes in detail the pretreatment and analysis procedures for metabolomic analysis of miso using GC-MS and is expected to serve as a useful guideline for conducting similar research in the future.