A photoresponsive molecularly imprinted system was prepared on a silicon wafer substrate surface via the host-guest complex of grafted 4-(3-triethoxysilylpropyiureido)azobenzene (TSUA) and mono-6-deoxy-6-((p-chlorosulfonyl)-benzoic acid)-beta-cyclodextrin (CBA-beta-CD), and the acid-base pair interactions/hydrogen bonds between CBA-beta-CD and the template molecules, including theophylline (TPE) and 4-hydroxybenzoic acid (4-HA). A molecular imprinting cycle "imprinting -> extracting -> uptaking -> shuffling" was also defined in the study, the processes of uptaking and shuffling were investigated in detail by equilibrium binding experiments, and the Langmuir adsorption isotherm and Scatchard equation were used to evaluate the binding affinity and the theoretical binding sites of the molecularly imprinted (MIS), nonimprinted (NIS), and pure (PS) silicon wafer substrates. Compared with the NISs and PSs, the MISs showed a significantly higher adsorption capacity for the template molecules More importantly, the MISs showed a reimprinted ability; after the process of shuffling, the molecularly imprinted, systems on the substrate surface were destroyed, and new imprinted systems could be fabricated for the recognition of other template molecules after washing the substrates under irradiation at 450 nm. Moreover, the selective adsorption for the MISs was investigated, which indicated that the MISs showed specific affinity to the template molecules (TPE or 4-HA).