The cell membrane-coated monolithic column (CMMC) ligand fishing assay is an interesting approach set up for the study of natural products (NPs). NPs such as Atractylodes lancea contain many compounds. Traditional methods used to separate compounds and determine active compounds by pharmacological tests are time-consuming and inefficient. Therefore, an alternative method is required to determine active compounds in NPs. Here, white blood cells were broken, and the white blood cell membranes (WBCMs) were immobilized on the surface of a monolithic column to form a CMMC. The column was characterized by Fourier transform infrared spectroscopy, scanning electron microscopy, and confocal laser scanning microscopy. Combined with gas chromatography/mass spectrometry (GC/MS), the CMMC was used to screen active compounds in Atractylodes lancea. Three potential active compounds including hinesol, β-eudesmol, and 4-phenylbenzaldehyde were discovered. A molecular docking assay demonstrated that these compounds could bind to MD-2 laid on WBCMs. In addition, antiinflammatory effects by the discovered compound in vitro were confirmed, and β-eudesmol showed a concentration-dependent inhibitory effect on the tumor necrosis factor (TNF)-α of a RAW264.7 cell (P < 0.05). The CMMC ligand fishing assay exhibits good selectivity, great speed effects and is a potentially reliable tool for drug discovery in NPs.