A metabolomics-based approach to the effects of vitamin D on allergic reactions was still unknown. A total of 111 children were enrolled and categorised based on their longitudinal vitamin D status (≥30 ng/ml, n=54; 20–29.9 ng/ml, n=41; <20 ng/ml, n=16). At the age of 3, 1H-Nuclear magnetic resonance (NMR) spectroscopy was used for urinary metabolomic profiling. Their connections with vitamin D levels, atopic indices, and allergies were investigated using integrative analysis and their functions in functional metabolic networks. 6 and 5 metabolites, respectively, were significantly linked with vitamin D status and atopic disorders (FDR-adjusted P-value<.05). Further association research found that 3-hydroxybutyric acid and glutamine, linked to vitamin D, were positively correlated with succinic acid and alanine, linked to the atopic disorder. Hippuric acid was also negatively correlated with atopic disease-associated formic acid, which was favorably correlated with vitamin D levels (P<.01). The absolute eosinophil count (AEC) was positively connected with serum IgE levels specific to Dpteronyssinus and Dfarinae (P<.01) but negatively correlated with vitamin D levels (P<.05). Vitamin D levels were substantially linked to amino acid metabolisms in children with allergies. According to integrative metabolomics research, vitamin D-related metabolites were linked to the gut microbiome and immune allergic reactions in children with allergies.