Caco-2 cell monolayer model was used to evaluate the intestinal permeability of 42 bioactive compounds in the famous traditional Chinese medicine (TCM) formula Gegen-Qinlian Decoction (GQD). These compounds include alkaloids, flavonoids and glycosides, triterpenoid saponins, and coumarins. Their transportations across the cell monolayers in the forms of herb extract and formula extract were monitored by liquid chromatography coupled with tandem mass spectrometry (LC/MS/MS) analysis. Most alkaloids from Huang-Lian; flavonoid C-glycosides from Ge-Gen and Huang-Qin; O-glycosides from Ge-Gen, Huang-Qin and Gan-Cao; O-glucuronides from Huang-Qin; and coumarins from Gan-Cao exhibited favorable permeability. Their PAB values were > 1.05 × 10−5 cm/s, and efflux ratios (ER, PBA/PAB) were ≤ 1.0. In contrast, triterpenoid saponins showed poor permeability (PAB ≤ 1.50 × 10−6 cm/s, ER ≤ 1.5), indicating a paracellular diffusion mechanism. Furthermore, GQD could remarkably improve the intestinal transport of alkaloids in Huang-Lian, flavonoid C-glycosides in Ge-Gen, as well as coumarins and flavonoid O-glycosides in Gan-Cao. These results indicate herb–herb interactions in GQD.