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Background: To understand the cumulative effect of topical formulations after medication, evaluate the therapeutic effect of microneedle-assisted (MN-assisted) paeoniflorin-loaded ethosomes (TGP-E), and explore the potential for deep penetration of drugs, this paper uses microdialysis to systematically study the percutaneous pharmacokinetics of TGP-E. Methods: First, optical coherence tomography (OCT) was used to study the effectiveness of microneedle puncture. Second, a microdialysis method and a UPLC-MS method for determining the amount of paeoniflorin (Pae) in dialysate were established. Finally, the transdermal pharmacokinetics of TGP-E was studied using in vivo microdialysis in rats under the above MN-assisted conditions. Results: The optimal 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 pharmacokinetic results demonstrated that the maximum drug concentration (Cmax) and the area under the curve (AUC) of the TGP-E gel were higher than the TGP-saline solution gel, and the mean retention time was lower. These indicated that microneedle can promote the entry of the ethosomes into the skin for in vivo experiments and greatly improve the possibility of deep penetration of the water-soluble Pae. Conclusion: Therefore, the microneedle-ethosomes delivery system is a more ideal means for promoting the deep penetration of Pae. These findings may provide a reference for the combination of multiple penetration-enhancement ways to promote drug absorption, and also provide a new insight to realize the development of novel, safe, and more effective dosage forms and administration routes of drugs. [ABSTRACT FROM AUTHOR]