Gegen Qinlian decoction (GQD), a traditional Chinese medicine used to treat infectious diarrhea, forms self-precipitates (GQD-P) during decoction. Although GQD-P and the supernatant (GQD-S) share an identical chemical composition, their physicochemical properties and in vivo behavior are not yet fully understood. This study aimed to investigate the physicochemical, in vitro, and in vivo properties of GQD-P, and to elucidate its unique role in the decoction's holistic efficacy. The morphology and pH-dependent dissolution of GQD-P were analyzed. Components in GQD, GQD-S, and GQD-P were quantified using HPLC, while pharmacokinetics of nine components were compared in rats administered GQD, GQD-S, or GQD-P using UPLC-MS/MS. GQD-P consisted of nanospheres whose dissolution was markedly enhanced under acidic, but not enzymatic, conditions. Baicalin and berberine were the main components of the primary precipitate framework. GQD-P components showed significantly prolonged MRT0-t and T1/2, and delayed Tmax compared to GQD-S. The whole decoction exhibited a biphasic profile combining features of both phases, with GQD-P acting as a pH-triggered, sustained-release reservoir. Together with the rapid-release supernatant, it creates a biphasic system prolonging systemic exposure and collectively underpins the comprehensive efficacy of GQD.