Investigation of the pharmacokinetics of paeonol microemulsion, microemulsion-based gels and marketed paeonol ointments by the skin-blood synchronous microdialysis coupled with LC/MS is reported in this study.  The microdialysis systems were established by linear probes and concentric circles probes.  In vivo recovery of paeonol in skin is (69.7 ± 4.8) % and in blood is (51.6 ± 7.2) %.  The paeonol microemulsion, microemulsion-based gels and marketed paeonol ointments were administered to rats. PBS (pH 7.4) served as perfused solution.  The perfusion rate was 5 μL·mL⁻¹ and the microdialysis samples were collected every 20 min intervals.  The paeonol concentration in perfused solution was determined by LC/MS.  The results showed that paeonol microemulsion and microemulsion-based gels significantly raised the drug concentrations in skin more than that of paeonol ointments.  The paeonol microemulsion-based gels has similar bioavailability as the paeonol ointments in blood, but its blood drug concentrations were steadier.  The paeonol microemulsion-based gels may be developed into a new preparation for dermis eczema.  The skin-blood synchronous microdialysis technique proved to be a new method for the pharmacokinetics study of transdermal delivery systems.