To compare the difference between liposome (LP) and microemulsion (ME) in delivering ibuprofen (IBU) transdermally and explore relative mechanism. IBU-LP and IBU-ME were prepared by ethanol injection and spontaneous emulsification, respectively. The percutaneous delivery was evaluated using Franz diffusion cells. Fourier transform infra-red spectroscopy (FTIR), differential scanning calorimetry (DSC), activation energy (Ea), and confocal laser scanning microscopy (CLSM) were used to investigate the transdermal mechanism. The particle size and encapsulation efficiency were 228.00 ± 8.60 nm, 86.68 ± 1.43%(w/w) for IBU-LP, and 56.74 ± 7.11 nm, 91.08 ± 3.27%(w/w) for IBU-ME. Percutaneous study showed that formulations enhanced permeation and drug retention in the skin. FTIR and DSC showed that the permeation occurred due to the interaction of the formulations with the lipid bilayer and the protein. The decrease in Ea (1.506 and 0.939 kcal/mol) revealed that the stratum corneum (SC) lipid bilayers were significantly disrupted and this destructive effect of IBU-LP was stronger. IBU-LP was superior to IBU-ME in the aspects of transdermal delivery of IBU.