Abstract: The use of gas chromatography/mass spectrometry (GC/MS) in the investigation of coal structure and identification for composition of small molecules was reviewed. Macromolecules and small molecules coexist in coals. Understanding the role of small molecules is the fundamental for effective, clean and value-added utilization of coals. For coals after treatments (extraction, oxidation and liquefaction), small molecules can be extracted from the macromolecular network and analyzed using GC/MS. Various kinds of organic species were identified using GC/MS, which gave explanation for coal structure, mechanism of coal liquefaction and oxidation.