The aim of this study was to investigate the effect of the Coptis chinensis, Glycyrrhiza uralensis, and fermented Glycine max (3Hb) extract on lipid barrier recovery and the alleviation of atopic dermatitis (AD). The 3Hb extract was administered to lipid barrier-eliminated mice (3HbT) for 5 days. Subsequently, the effect of the 3Hb extract on general skin features and the regulation of filaggrin, inflammatory response, Th2 differentiation, and the skin micro-environment for defense, was evaluated. In the 3HbT, filaggrin was effectively recovered. The clinical skin score was significantly lower in the 3HbT compared with control groups. In addition, significant decreases in pH and TEWL as well as in the levels of kallikrein 7, PAR-2, TSLP, IL-4, Fc ε receptor, and phosphate-NF-κB p65 were observed in the 3HbT, compared with the other control groups. Further, compared with control groups, the 3HbT showed a significant increase in those of claudin, cathelicidin, TLR, and NHE-1. Our results indicated that the 3Hb extract effectively recovered filaggrin. Through the recovery of filaggrin, inflammation and the Th2 differentiation process can be regulated, and microenvironments for defense can be recovered. Therefore, we confirmed the potential of the 3Hb extract for use in the proactive therapy of AD.