Herbal patches are widely used in clinics for their good curative effects. However, due to the complexity of plant matrices and the extremely low content of transdermal components, the individuation of their effective bioactive compounds represents a challenge: there is then a great need for an efficient method to reveal the bioactive ingredients of herbal patches. In this work, a wide-screening approach is proposed to an individuation of transdermal bioactive components in herbal patches obtained by Spatholobus suberectus Dunn (S. suberectus). Using a two-dimensional microscale carbon fiber/active carbon fiber system combined with a quadrupole time-of-flight high-resolution mass spectrometry (2DµCFs-QTOF-HRMS), a rapid and comprehensive analysis, lasting only 5 min, allowed the identification of 45 distinct polar components within S. suberectus extracts. Among these, 30 components exhibited a transdermal penetration estimated at values higher than 10 %. The key target, predicted by bioinformatics, was prostaglandin-endoperoxide synthase 2 (PTGS2). From the transdermal components of S. suberectus, four potential inhibitors of PTGS2 (protocatechuic acid, isoliquiritigenin, medicarpin, and catechin) were screened by multi-chamber membrane separation electrophoresis (MCMSE). The presence of binding pockets and action sites for medicarpin, isoliquiritigenin, and catechin determines higher binding energy towards PTGS2, with lower IC50 values (12.27, 9.08, and 41.68 μM, respectively). The high-throughput and high-sensitivity analysis by 2DµCFs-QTOF-HRMS, combined with a high-accuracy screening of MCMSE, provides strong technical support for the discovery of trace transdermal bioactive components of herbal patches. The integration of the two technologies could accelerate the study of action mechanisms, quality control, and product improvement of herbal patches.