The paper deals with the preparation of silica adsorbent with nanopores and its selective separation of genistein from the crude solution. According to the molecular recognizing technique, a new silica adsorbent was prepared which took the genistein as the template molecule, the γ-aminopropylthriethoxysilane as the functional monomer which can react with the phenolic hydroxyl and the tetraethyl orthosilicate as the cross-linker. The adsorbent was charactered by the BET, FTIR, TEM measurements, the static adsorption experiment, selective adsorption experiment and elution experiment. The results show that the adsorbent has high specific area, special selectivity and high adsorption capacity for genistein. There are lots of nanopores uniformly distributed in the adsorbent which match the shape of the template molecule. New bonds are formed with adsorbent and the genistein. It is concluded that the ability of the adsorbent to bind genistein is a result of both specific size and shape of the nanopores in this adsorbent consisting with the correct position of the functional groups involved in the template binding through ionic and hydrogen interactions, and the nanopores lead to the best performance in the adsorption experiment