Human milk oligosaccharides (HMOs) and the milk fat globule membrane (MFGM) represent novel treatments for cow's milk allergy (CMA). They exhibit the beneficial attribute of diminishing nutrient damage when compared to conventional enzymatic digestion of milk proteins. However, the effects and mechanisms underlying the synergistic interaction between HMOs and the MFGM in allergy treatment remain unclear. Consequently, this study was undertaken to assess the protective properties of HMOs and the MFGM against CMA and to elucidate their potential mechanisms in a mouse model of β-lactoglobulin (BLG)-induced allergy. The findings demonstrated that HMOs and the MFGM could significantly reduce the allergy score and splenic index, and they diminished the levels of inflammatory mediators (total immunoglobulin E (IgE), specific IgE, histamine, and mMCP-1), while concurrently bolstering tight junctions (ZO-1, claudin-1, and occludin), and reducing intestinal permeability. Notably, HMOs and the MFGM exhibited optimal synergy. In addition, HMOs and the MFGM synergistically mitigated the immune response to Th2 overactivity in allergy by the promotion of Th1 and Treg cell responses, thereby suppressing the levels of inflammatory cytokines IL-4 and IL-5. Analysis of the gut microbiota and its metabolic activities revealed that HMOs and the MFGM increased the abundance of Lactobacillus and Butyricicoccus, leading to higher production of butyrate. Furthermore, these beneficial bacteria and the resultant butyrate also contributed to the suppression of allergy-associated bacterial populations such as Desulfovibrio and Rikenellaceae. In summary, HMOs and the MFGM acted in synergy to modulate inflammatory responses and ameliorate barrier damage, contributing to the mitigation of CMA, a process potentially linked to gut microbiota dynamics and the resultant butyrate metabolism. This effect may be related to the gut microbiota and its metabolic production of butyrate.