Paeoniflorin, the main component of total glucosides of paeony (TGP), shows good therapeutic effects in arthritis, but has low bioavailability when administered orally. Avoiding such a deficiency for topical administration would expand its clinical application. This study aimed to avoid these limitations by using nanotechnology (ethosomes) and a physical approach (microneedles). Paeoniflorin-loaded ethosomal formulation (TGP-E) was optimized and evaluated in terms of entrapment efficiency (EE), particle size (PS), zeta potential (ZP), polydispersity index (PDI) and morphology. TGP-E was prepared by the hot injection method and optimized by single-factor tests and an orthogonal experimental design. The optimized paeoniflorin-loaded ethosomes had EE of 27.82 ± 1.56%, PS of 137.9 ± 7.57 nm with PDI of 0.120 ± 0.005, ZP of −0.74 ± 0.43 mV. Ethosomes showed a nearly spherical shape under the transmission electron microscope (TEM). The optimal microneedle-assisted (MN-assisted) conditions were obtained at a microneedle length of 500 μm, a pressure of 3 N and an action time of 3 min. The cumulative penetration amounts (Qn) of TGP solution transdermal (ST) and MN-assisted TGP solution transdermal (MST) were 24.42 ± 8.35 μg/cm2 and 548.11 ± 10.49 μg/cm2, respectively. Qn of TGP-E transdermal (PT) and MN-assisted TGP-E transdermal (MPT) were 54.97 ± 4.72 μg/cm2 and 307.17 ± 26.36 μg/cm2, respectively. These findings indicate that use of ethosomes and microneedles can both enhance the penetration ofpaeoniflorin, but for the water-soluble drug, there is no obvious synergism between nanotechnology and microneedles for enhancing penetration in a transdermal drug delivery system.