〔Abstract〕 Objective To investigate the metabolic alterations of serum short chain fatty acids (SCFAs)in pediatric patients with atopic dermatitis (AD)and their correlation with different clinical phenotypes using targeted metabolomics. Methods This study enrolled 87 AD patients and 67 healthy controls (HC). Serum levels of eight SCFAs were quantified by ultra-high-performance liquid chromatography-mass spectrometry.The associations between SCFAs and AD were assessed using various statistical methods.Results Compared with the HC group,levels of acetic acid (AA), propionic acid (PA), and caproic acid (CA) (P=0.002，P=0.002，P=0.043) decreased in the AD group. Logistic regression analysis identified AA (OR = 0.449, 95% CI: 0.289–0.698) and PA (OR= 0.487, 95% CI: 0.324–0.732) as protective factors against AD. The combination of AA and PA yielded an area under the curve (AUC) greater than 0.7, indicating good diagnostic efficacy.Age stratified analysis revealed that AA reduction was predominant in childhood, whereas PA reduction was predominant in adolescence. Pathway enrichment analysis showed significant enrichment of fatty acid biosynthesis (FDR = 0.341,P = 0.003) and vitamin K metabolism (FDR = 1,P = 0.039) pathways. Furthermore, subgroup analyses based on disease severity, personal /family history of atopy, and sex revealed no significant differences in SCFAs levels among the groups. Conclusion Differential serum SCFAs and their enriched metabolic pathways may be implicated in the pathogenesis of Atopic Dermatitis.