Atopic dermatitis is a common chronic, relapsing, inflammatory skin disease; however, its pathogenesis remains unclear. The theory of "clear-turbid interference" originates from the Inner Canon of Yellow Emperor and refers to a pathological condition in which clear yang and turbid yin intermingle, and qi movement becomes disordered. This paper elucidates the theoretical connotation of "clear-turbid interference" and its core mechanism in triggering atopic dermatitis, as well as the role of the "gut-skin axis" in atopic dermatitis development. Internal dampness-turbidity and disharmony between ying and wei constitute the core pathological mechanisms linking clear-turbid interference to atopic dermatitis. Treatment for different stages and syndromes should be guided by syndrome differentiation. For example, for spleen deficiency with a dampness syndrome in subacute or chronic stages, Chushi Weiling Decoction may be used to fortify the spleen, eliminate dampness, lift the clear, and downbear the turbid. For patterns with prominent heat manifestations, such as dampness-heat immersion or heart fire with spleen deficiency, bitter-cold dampness-drying herbs can be added on this basis. For wind-dampness-heat accumulation in the acute stage, Mahuang Lianyao Chixiaodou Decoction can be used to release the exterior, expel pathogens, and harmonize ying and wei. In cases of spleen deficiency with blood dryness or liver-kidney insufficiency during the chronic stage, in addition to nourishing yin to moisten the skin and tonifying the liver-kidney, wind-medicinals should also be employed to open the sweat pores and promote qi movement. These approaches restore the physiological state without clear-turbid interference while regulating intestinal flora, providing new approaches and perspectives for integrating traditional Chinese and Western medicine in treating atopic dermatitis.