Currently, the need for safe and effective methods for relieving allergies is an important concern. In this study, we evaluated the role of Lactobacillus rhamnosus GG (LGG) in alleviating β-conglycinin (β-CG)-induced allergies and elucidated the related molecular mechanisms. Typical allergy symptoms and inflammatory factors in the serum showed that LGG intervention effectively alleviated β-CG induced allergy in mice, which was better than natural recovery (NR). Intestinal villi were restored and lower levels of CD4+ T cells infiltrated after LGG intervention. We evaluated whether LGG intervention weakened the proliferation ability of the spleen cells of allergic mice, balancing between T/B cells and Th1/Th2 and Th17/Treg cytokines. Transcriptome analysis revealed that 4106 differentially expressed mRNAs were identified by comparing the LGG group and β-CG group, and 546 differentially expressed mRNAs were identified by comparing the LGG group and NR group. KEGG pathway analysis identified that the T cell receptor (TCR) signaling pathway was significantly enriched upon LGG intervention, and the upregulated Ifnar2 and the downregulated Tgfbr2, Il13r2 and Il4ra were further validated by qPCR analysis. Therefore, the above results fully revealed the important role of LGG in alleviating β-CG-induced allergies.