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Background: The incidence of allergic disease remains high, and many studies have focused on the association between food diversity in infancy and allergic disease later in life, but their conclusions are still controversial. Objective: We aimed to synthesize the literature on the association between childhood diet diversity and atopic disease. Methods: We searched the PubMed, Cochrane Library, Embase, Scopus, VPCS, and Wanfang databases for studies about food diversity and atopic disease. Seventeen high-quality studies, 14 cohort studies, and 1 case–control study were included from 5244 studies with sample sizes ranging from 100 to 5225. Results: All high-quality cohort studies showed that increasing food diversity in infancy can effectively prevent the occurrence of food allergies (5/5). Moderate evidence showed that increased food diversity reduced the risk of asthma (4/6), food sensitization (3/5), and atopic dermatitis (3/5). However, its effect on eczema (5), allergic rhinitis (4), and other diseases remains controversial. Conclusions: Increasing food diversity during infancy is a potential method for preventing food allergy, asthma, atopic dermatitis, and food sensitization later in life. There is little or no comparative evidence about the protective effect of food diversity on other atopic diseases.