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Many probiotic bacteria have been proven to prevent allergic airway responses through immunomodulation. This study was conducted to evaluate the effects of heat-killed Bifidobacterium longum BBMN68 (BBMN68) in pasteurized yogurt on the alleviation of mugwort pollen (MP)-induced allergic inflammation. BALB/c mice aged 5–6 weeks were randomly assigned and fed pasteurized yogurt containing heat-killed BBMN68 for 27 days, followed by allergic sensitization and challenge with MP extract. The allergic mice that received pasteurized yogurt containing heat-killed BBMN68 had improved immune status, including a lower serum IgE level, decreased serum interleukin (IL)-4, IL-5, and IL-13 concentrations, and alleviated airway inflammation manifested by increased macrophage and decreased eosinophil and neutrophil counts in BALF, as well as airway remodeling and suppressed peribronchial cellular infiltration. Moreover, oral administration of pasteurized yogurt containing heat-killed BBMN68 significantly modulated gut microbiota composition by influencing the proportion of beneficial genera associated with inflammation and immunity, such as Lactobacillus, Candidatus_Saccharimonas, Odoribacter, and Parabacteroides, which also negatively correlated with serum IgE and Th2 cytokine levels. These results demonstrated that pasteurized yogurt containing heat-killed BBMN68 had mitigative effects on allergic airway inflammation, likely through maintaining the systemic Th1/Th2 immune balance by altering the structure and function of the gut microbiota.