Alopecia affected approximately 16.6% of all people in China, however, treatment options remain limited due to the side effects. Plant bioactive compound baicalin (BC) possesses hair growth-promotion activity, but poor water solubility and unsuitable log P value restrict its topical application, and natural Glycyrrhizin (GL) can exactly overcome these drawbacks. Here, BC was encapsulated in GL to form GL-BC micelles for alopecia treatment. Simultaneously, tween 80 (TW) as carriers was incorporated in the GL-BC to form GL-TW-BC micelles. The topical penetration, penetration pathways, cellular uptake and the underlying mechanisms behind the hair loss reconstruction of the GL micelles were investigated. We found the optimal GL-BC and GL-TW-BC formulations significantly improved the penetration and accumulation of BC in the porcine skin predominantly through the hair follicles pathways without causing skin irritation, which resulted in a targeted treatment. The proliferation of human dermal papilla cells (hDPCs) and effective cellular uptake was also enhanced. Moreover, the activation of the Wnt/β-catenin pathway, up-expression of vascular endothelial growth factor (VEGF), α-melanocyte-stimulating hormone (α-MSH) and interleukin-10 (IL-10) were the mechanisms of micelles for the hair recovery. Interestingly, GL and BC exhibited a synergistic treatment of alopecia. Collectively, GL-BC and GL-TW-BC can be used as promising approaches for the treatment of alopecia.