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BACKGROUND: Atopic dermatitis (AD) is a chronic inflammatory skin disorder characterized by pruritus and eczema lesions and psychiatric comorbidities. The gut–brain–skin axis plays a pivotal role during AD development, which might suggest a novel therapeutic strategy for AD. The present study aims to uncover the protective effects and underlying mechanisms of fructo‐oligofructose (FOS), a type of prebiotic, on AD‐like skin manifestations and comorbid anxiety and depression in AD mice. RESULTS: Female Kunming mice were treated topically with 2,4‐dinitrofluorobenzene (DNFB) to induce AD‐like symptoms and FOS was administered daily for 14 days. The results showed that FOS could alleviate AD‐like skin lesions markedly as evidenced by dramatic decreases in severity score, scratching bouts, the levels of immunoglobulin E (IgE) and T helper 1(Th1)/Th2‐related cytokines, and the infiltration of inflammatory cells and mast cells to the dermal tissues. The comorbid anxiety and depressive‐like behaviors, estimated by the forced swimming test (FST), the tail‐suspension test (TST), the open‐field test (OFT), and the zero maze test (ZMT) in AD mice, were significantly attenuated by FOS. Fructo‐oligofructose significantly upregulated brain neurotransmitters levels of 5‐hydroxytryptamine (5‐HT) and dopamine (DA). Furthermore, FOS treatment increased the relative abundance of gut microbiota, such as Prevotella and Lactobacillus and the concentrations of short‐chain fatty acids (SCFAs), especially acetate and iso‐butyrate in the feces of AD mice. The correlation analysis indicated that the reshaped gut microbiome composition and enhanced SCFAs formation are associated with skin inflammation and behavioral alteration. CONCLUSION: Collectively, these data identify FOS as a promising microbiota‐targeted treatment for AD‐like skin inflammation and comorbid anxiety and depressive‐like behaviors. © 2023 Society of Chemical Industry. [ABSTRACT FROM AUTHOR]