Atopic dermatitis (AD) is a chronic inflammatory skin disorder affecting up to 10-20% of children worldwide. Since the diagnosis of AD is typically based on a set of clinical symptoms and features, it is necessary to discover useful biomarkers that can complement the conventional method at the molecular level. In this study, we aimed to identify specific metabolites that could distinguish children with AD from healthy individuals. As metabolites are the end products of the cellular regulation process, their levels are closely related to various pathological states. We profiled metabolites in the serum of AD children and healthy children aged 6 to 8 years using an ultra-performance liquid chromatogram coupled with a mass spectrometry system. We selected 44 metabolites for the diagnosis of AD based on the results of the comparative metabolomics analysis. Most observed metabolite changes are related to glycerophospholipid metabolism. Surprisingly, the serums levels of all screened lysophospholipid (lysoPC and lysoPE) were significantly decreased in children with AD compared to healthy control, suggesting that they could be a reliable biomarker of AD diagnosis. Furthermore, these metabolites were significantly correlated with the serum concentration of total IgE, D.f-IgE, and eosinophil. Taken together, our findings suggest potential biomarkers useful for the identification of AD and may provide a clue to the pathogenesis of AD.