Atopic dermatitis (AD), a chronic relapsing inflammatory pruritic skin disorder with a unique pathophysiology, has a high incidence in the perioral zone among infants. This study aimed to analyze the association of skin microfloral dynamics with disease severity and treatment of AD in 0-1-year-old infants. Based on the eczema area and severity index, subjects were divided into five groups, i.e., mild, moderate, severe, and severe post-treatment, with a healthy control group, and bacterial density at the perioral lesion, disease severity, and treatment were assessed in 0-1-year-old infants with AD. The perioral lesions were colonized predominantly by Firmicutes, followed in abundance by Proteobacteria, Actinobacteria, and Bacteroidetes. In the phylum Firmicutes, Streptococcus was the most predominant genus. In AD infants, the abundance of Bacteroidetes and Fusobacterium decreased significantly with an increase in disease severity (p < 0.01). The abundance of 6 genera, including Prevotella, decreased significantly with an increase in disease severity (p < 0.05). The abundance of Prevotella melaninogenica decreased gradually with an increase in disease severity and increased after treatment; this trend was reversed for Corynebacterium simulans. A reduction in the abundance of Staphylococcus and an increase in that of skin microflora including Prevotella spp., Staphylococcus epidermidis, and Erwinia dispersa were associated with treatment and clinical improvement. Skin bacterial composition varies with AD severity, and Corynebacterium simulans and Prevotella melaninogenica are positively and negatively correlated with AD severity, respectively. This study provides a theoretical basis to identify potential biomarkers AD occurrence and pathogenesis.