Atopic dermatitis (AD) is a chronic, relapsable and pruritic skin disease, commonly found in children and adolescents. The prevalence of AD is increasing worldwide. It is reported that AD is related to many factors such as genetic inheritance, environment, immunity and skin barrier dysfunction, suggesting a very complex pathogenesis. In recent years, high-throughput technologies in the field of genomics and metabolomics have opened up new perspectives on the pathogenesis of AD, and shown potential application prospects in microbiome transplantation therapies for AD. This review summarized the current advances in the relationship between skin microecology and skin health, the pathogenesis and microbiomic characteristics of AD, features of pathogenic microorganisms, and microbiome transplantation therapies for AD. Based on our own practical experience, we put forward a culturomics research protocol to study the human skin microbiome and a method for quantitative microbiological examination, aiming to provide reference for the prevention, clinical treatment and therapeutic monitoring of AD.