Co-immunoprecipitation is a very effective method for studying protein-protein interactions. However, the preparation of antibodies in this method involves the injection of antigen into mammals, and requires the use of the expensive protein A-Sepharose 4B. Molecular imprinting polymer can compensate for these deficiencies. In this paper, a new strategy for studying protein interactions is reported; this method is based on the use of protein-imprinted polymers (PIPs). PIP is a proper substitute for antibody. We designed and synthesized assistant recognition polymer chains (ARPCs), which were limited length polymer chains with randomly distributed recognition and immobilizing sites. The template protein was selectively assembled with ARPCs. The assemblies were adsorbed by macroporous microspheres, and were immobilized by cross-linking polymerization. After removing the templates, the two kinds of synthesized PIPs were used to adsorb natural BiP or FKBP23 from ER extract; both showed high selectivity. Furthermore, we investigated the binding specificity of BiP to FKBP23, using synthesized PIPs. The results showed that FKBP23 could bind to BiP in ER in a process regulated by the concentration of Ca(2+), which was consistent with the immunoprecipitation results. This strategy may provide a general solution for investigating protein interactions.