Direct application of monolithic column of molecularly imprinted polymers (MIPs) for selective separation and purification of protocatechuic acid from the crude extract of seeds of Cirsium segetum Bunge was attempted in present work. An in-situ polymerization technique was used for the preparation of MIPs monolith using protocatechuic acid as the template, acrylamide as functional monomer, 1,1,1-Trimethylolpropane trimethacrylate (TRIM) as cross-linker, and a mixture of tetrahydrofuran-iso-octane (1:2, v/v) as porogenic agents. The preparation procedure was optimized and the retention behavior and selectivity of this monolith evaluated by chromatographic analysis. Then, this monolith was directly connected into the liquid phase chromatographic system to trap target molecule from crude extract. Results indicated its high selectivity for protocatechuic acid, good affinity to its structurally related compounds, and good workability in herb matrix. Sample matrix compounds in a crude extract of this plant could be removed by carefully washing with a solvent, and protocatechuic acid was purified simultaneously by selective desorption with the eluent. The purity and recovery of product obtained can reach 98.7% and 86.1%, respectively.