The oral bioavailabilities of phenolic acids in Flos Lonicerae Japonicae beverage were low. The observation from an in vitro Caco-2 cell model showed that the absorptions of phenolic acids were mainly permeated via paracellular diffusion, and influenced by P-glycoprotein (P-gp), multidrug resistance-associated protein 2 (MRP2) and breast cancer resistance protein (BCRP). Besides, the Papp (AP→BL) values in Flos Lonicerae Japonicae were significantly higher than those of monomers, which was attributed to the decrease of efflux ratios (<1.0) influenced by flavones (luteoloside and luteolin) on the P-gp, but they were still poorly absorbed. The results indicated that the absorptions in Flos Lonicerae Japonicae as well as those of monomers were mainly restricted by the tight junctions (TJs). Food supplements (honey and propolis) or edible excipient (chitooligosaccharide) as TJ enhancers will be investigated to improve the functions of Flos Lonicerae Japonicae healthy beverages.