Sensitive skin is defined as skin with low tolerance and high reactivity. Natural products, such as paeoniflorin and madecassoside, have unique skin care functionality. However, because they are hampered by the skin barrier, paeoniflorin and madecassoside have difficulty penetrating the stratum corneum, resulting in weakened skin barrier repair and anti-inflammatory effects. In addition, there is a lack of detailed studies on the efficacy of paeonol and madecassic in human skin, especially in 3D skin models and clinical trials. To overcome the low transdermal delivery issue, we developed nanoemulsions (PM-NEs) loaded with paeonol and madecassoside to improve their delivery efficiency and promote sensitive skin repair and anti-inflammation effects. Furthermore, systematic evaluations of the efficacy in cell line models, 3D skin models, and clinical trials were conducted. The PM-NEs effectively improved the efficacy of paeonol and madecassoside glucoside transdermal penetration and retention and enhanced cellular uptake. Cellular assays and 3D epidermal models showed that the PM-NEs significantly promoted the secretion of filamentous protein, aquaporin 3, Claudin-1, and hyaluronic acid, and considerably inhibited the secretion of interleukin 1α, interleukin 6, tumor necrosis factor-α, and prostaglandin E compared to free components. Notably, clinical trial data showed that the PM-NEs significantly reduced transepidermal water loss, a* values, erythropoietin, the amount of non-inflammatory acne, and the amount of inflammatory acne in the facial skin. Three levels of systematic studies suggest that co-delivery of paeoniflorin and madecassoside via nanoemulsions is a promising strategy to improve topical delivery efficiency and anti-inflammatory repair efficacy in sensitive skin.