The invention discloses a nucleic acid aptamer functionalized POSS (polyhedral oligomeric silsesquioxane) crosslinking organic-silica gel hybridization monolithic column, and a preparation method thereof. The monolithic column is a compatible monolithic column formed in a way that highly-hydrophilic organic polymerized monomer, POSS, acrylic ester cross-linking agent, nucleic acid aptamer aqueoussolution and initiator are dissolved through ternary pore-forming agent to form homogeneous solution; the homogeneous solution is injected into the column to synchronously generate free radical thermal-initiation polymerization and 'sulfydryl-alkene' click chemistry reaction to be directly prepared; the ternary pore-forming agent is mixed solution formed by three ingredients of aqueous-N,N-dimethyl formamide-PEG (polyethylene glycol) 10000. The nucleic acid aptamer is bonded by covalent bonds through a one-step method, and the prepared compatible monolithic column has the advantages of stablestructure and simple and quick method and is suitable for the specific recognition separation of ochratoxin A.