Metabolomics can provide a readout of the biochemical and physiological state of a biological system. Gas chromatography coupled to mass spectrometry (GC-MS) has been widely applied for metabolomic analysis due to its numerous advantages, such as good sensitivity, high resolution, reproducibility, extensive database, lower acquisition cost and greater coverage. In addition, combined with efficient methods of sampling and sample preparation, the metabolomic analysis of damaged skin based on GC-MS can provide an important step toward elucidating several skin diseases. Based on this, this review presents a comprehensive overview of sampling, sample preparation, data processing and GC-MS analysis of metabolomic studies of damaged skin. Also, part of the biological interpretation of metabolites such as cis- and trans-urocanic acid (UCA) altered in photoexposed skin and lauric acid (C12:0) and palmitic acid (C16:0) in melanoma is discussed. Finally, to improve decision-making, a part of the integration of skin metabolomics with other omics sciences for the advancement of diagnosis is presented.