Zhu-Ling decoction (ZLD), a classical traditional Chinese medicine (TCM) formula, is used for the treatment of chronic kidney diseases. However, the structure and activity of absorbed oligosaccharides (OSs) in ZLD are not clear. In this study, a novel strategy with in vivo characterization, extraction, isolation, activity evaluation was established and applied to identify absorbed anti-inflammatory OSs in ZLD. The results revealed that 30 OSs (22 reducing and 8 non-reducing OSs) and 11 OSs (7 reducing and 4 non-reducing OS) were characterized from ZLD in vitro and in vivo by using UPLC/Q-TOF-MS with PMP derivatization, respectively. Among them, a series of −1 → 3-β-D-Glcp-OSs were isolated and identified by HPLC-HILIC-UVD-ELSD, SPHPLC-HILIC-RID, monosaccharide composition, MS and 1D/2D-NMR spectroscopy, including laminaritriose, laminaritetraose, laminaripentaose, laminarihexaose, laminariheptaose, laminarioctaose and laminarinonaose. Moreover, the 4 non-reducing absorbed OSs were identified by comparison with reference standards, including sucrose, trehalose, raffinose and stachyose. Among them, laminaritriose, laminaritetraose and laminaripentaose significantly inhibited TNF-α and IL-6 levels in LPS-induced HK-2 cell and exerted significant anti-inflammatory effects via the NF-κB and Akt/mTOR signaling pathways. Together, our work provides a novel strategy for discovery of absorbed anti-inflammatory OSs and broadens new horizons for the discovery of in vivo pharmacodynamic substances in TCM formulas.