In order to compare the preventive effects of wheat hydrolyzed peptide as well as probiotics and their mixtures on wheat allergy in young mice, and to assess whether there is a synergistic effect between probiotics and wheat hydrolyzed peptide, a wheat allergy model was established by observing the body mass, rectal temperature, visceral index, and jejunum pathological sections of the young mice, and detecting the levels of their serum-specific immunoglobulin E (IgE) and specific immunoglobulin G1 (IgG1), specific immunoglobulin G2a (IgG2a) levels, and their spleen cytokine interleukin 4 (IL-4), interleukin 5 (IL-5), interleukin 13 (IL-13), and gamma-interferon (IFN-γ) levels were determined. The results showed that early digestive intake of wheat hydrolyzed peptides significantly increased the thymus index and spleen index of young rats; significantly decreased the serum specific IgE level and specific IgG1 level (P < 0.01); significantly decreased the spleen IL-4 level (P < 0.05) and IL-13 level (P < 0.01); significantly increased the spleen IFN-γ level (P < 0.01); and significantly rebounded the rectal temperature of young rats (P < 0.01); significantly rebound rectal temperature in young rats (P < 0.01). Early digestive tract intake of probiotics and wheat hydrolyzed peptide mixture significantly inhibited the shifting of helper T-cell 2 (Th2) type response, with significant reduction of IL-5 level and Th2/Th1 ratio; and had a significant effect on the alleviation of jejunal pathology, such as jejunal villus breakage, shallow depth of crypt, and low height of villi. In conclusion, the synergistic wheat hydrolyzed peptide and probiotic wheat hydrolyzed peptide mixture has the potential to prevent wheat allergy in young mice, and it is expected to be used in the development of formulas for special medical purposes to prevent wheat allergy in infants and young children.