OBJECTIVE: The aim of this study is to analyze the clinical effect of standardized dietary avoidance therapy on children with cow milk protein allergy (CMPA) and its effect on the intestinal flora. METHODS: The clinical data of 200 children with CMPA from our hospital from February 2020 to May 2021 were collected, and they were divided into a study group ( = 100) and a routine group ( = 100) based on different intervention modalities. The routine group received routine treatment, whereas the standardized dietary avoidance therapy was used in the study group. The clinical effects and related intestinal microflora indexes of the two groups were analyzed and compared. RESULTS: There was no significant difference in the incidence of related symptoms between the two groups before intervention ( > 0.05), and the conditions of the two groups were improved after intervention. The incidences of skin (2%), digestive tract (3.00%), and respiratory tract (1.00%) in the study group were significantly lower than those in the routine group (14.00%, 18.00%, and 11.00%) ( > 0.05). The time taken for complete remission of symptoms and milk tolerance months in the study group (41.23 ± 23.68, 13.28 ± 6.17) were significantly shorter than those in the routine group (145.14 ± 66.74, 16.17 ± 8.05) ( > 0.05). The values of height, weight, and head circumference (HC) of children in the study group (79.88 ± 2.18, 11.09 ± 1.34, 47.88 ± 0.63) were higher than those in the routine group (76.21 ± 2.34, 9.81 ± 1.18, 45.98 ± 0.59) ( > 0.05). The levels of and (9.95 ± 0.89, 11.31 ± 1.05) in the study group were higher than those in the routine group (9.11 ± 0.74, 10.38 ± 0.94), and the levels of yeast-like fungi in the study group (3.08 ± 0.24) were lower than those of the routine group (3.82 ± 0.31) ( > 0.05). CONCLUSION: The standardized dietary avoidance therapy is remarkable in the treatment of CMPA, in which the children were able to tolerate ordinary milk earlier, and the intestinal flora was significantly improved, thereby promoting the growth and development of children. It therefore merits clinical promotion.