The skin of atopic dermatitis (AD) patients exhibits a striking susceptibility to colonization and infection with Staphylococcus aureus. This review summarizes our understanding about the role of S. aureus in AD. Indeed, S. aureus colonization is both a cause and a consequence of allergic skin inflammation. The mechanisms that allergic skin inflammation of AD promotes the increase of S. aureus colonization include skin barrier dysfunction, increased synthesis of the extracellular matrix adhesins for S. aureus, and defective innate immune responses due to decreased production of endogenous antimicrobial peptides. On the other hand, the exotoxins secreted by S. aureus are superantigens. Staphylococcal superantigens (SsAgs) may penetrate the skin barrier and contribute to the persistence and exacerbation of allergic skin inflammation in AD through the stimulation of massive T cells, the role of allergens, direct stimulation of antigen-presenting cells and keratinocytes, the expansion of skin-homing cutaneous lymphocyte-associated antigen-positive T cells, and the augmentation of allergen-induced skin inflammation. SsAgs also induce corticosteroid resistance. In therapeutic interventions, anti-inflammatory therapy alone is very effective in reducing S. aureus colonization on the skin, but antibiotic treatment alone is unable to improve the allergic skin inflammation of AD. Therefore, we recommend the combination therapy of anti-inflammatory drugs and antibiotics in the AD patients with secondary bacterial infection, exacerbated AD, or poorly controlled AD. However, when AD is well controlled by anti-inflammatory drugs alone, we do not recommend the antibiotic therapy.